I don't have much to add to mweiss' nice answer in terms of teaching suggestions. But I would like to add my own point of view on what the abuse of notation $\mathbf{r}=\mathbf{r}(s)=\mathbf{r}(t)$ means and where it comes from historically.
The first person to do this abuse of notation (implicitly) seems to have been Jacobi around 1830 (I suggest you read that link after reading the rest of what I'll say). Note that 1830 is more than 100 years after Bernoulli and Euler introduced the notation $y=f(x)$ and more than 140 years after Leibniz startet to talk of functions. In the period between Leibniz and Jacobi we find luminaries like Euler, Lagrange, Laplace, Fourier, Bolzano, Cauchy and Gauss who, as far as I can tell, never did this. So it's not the case, as some people believe, that mathematicians and physicist have been writing $y=y(x)$ ever since the invention of functions. Even after Jacobi there are many people, like Riemann, Peano or Planck who apparently didn't do it. So it's also not the case that physicists invented $y=y(x)$ or somehow need it more urgently than mathematicians.
So why did Jacobi start doing it? In the above link you can read what he himself had to say about it (I highly recommend it to anyone teaching multivariable calculus), but his own words actually don't explain it completely. To understand it better we first need to understand how the word function was used prior to about 1900. Most mathematicians seem unaware of the dramatic change of meaning this word underwent during the period 1900-1920. And it's a non-trivial task for a modern mathematician with a set theoretic perspective to make sense of what it meant prior to 1900. But let's try.
If you open any calculus textbook written after Leibniz and before at least 1910 (a ~200 year period) you'll find that the word "function" is always defined as function of something. Here is a typical example from the end of that period taken from Peano's Calcolo differenziale e principii di calcolo integrale 1884, p.3:
Among the variables there are those to which we can assign
arbitrarily and successively different values, called independent
variables, and others whose values depend on the values given to the
first ones. These are called dependent variables or functions of
the first ones.
We shall first treat functions of a single independent variable, and
we shall say that: a function $y$ of $x$ is given in an interval
$(a, b)$, if to any value of $x$ in between $a$ and $b$ corresponds a
unique and determinate value for $y$ - whatever the means of
determining it.
So for example $x^{2}$ is a definite function of $x$ for any value of
$x$, and is hence given in any interval; $\sqrt{x}$ understood as the
arithmetic root of $x$, is given for all positive values of $x$ ;
while $\frac{1}{1} + \frac{1}{2} +\frac {1}{3} +\cdots + \frac{1}{x}$
is a function of $x$ defined only for integer and positive values of
the variable, etc.
So a function, like $x^2$ or $y$, is a variable quantity, just like $x$, only that it satisfies some additional property. If you feel uncomfortable with "$y$ is a function of $x$" because you are so used to modern functions, maybe paraphrasing it as "$y$ depends on $x$" helps a bit. (Certainly if $f:\mathbb{R}\to \mathbb{R}$, no modern mathematician would say that $f$ depends on $x\in \mathbb{R}$.) Hence whenever they called something a function, they had to add of what that thing is a function. But often it was clear from the context or the notation, so they would soon drop the "of $x$" and simply talk of functions. So for example on p.13 we find Peano writing
One says that a function $f(x)$ becomes maximal relative to an
interval $(a,b)$ when $x=x_0$...
To be correct he should have said something like: "One says that a function of $x$, $f(x)$, becomes ...". But it was clear form the notation. (Observe that nothing prevents $f(x)$ from being a function of something else too. For example when $x$ is itself a function of $t$, then $f(x)$ would also be a function of $t$.) We inherited the phrase "$f(x)$ is a function" —which we find in every modern calculus textbook (and btw. you used the question)— from this pre 1900 period, even though according to our modern convention we should correctly say "$f$ is a function".
To emphasise again the difference between "function of ..." and our modern "functions": when $y=f(x)$ they called $y$ and $f(x)$ a function, while we call $f$ a function.
If they called $f(x)$ the function, how did they call $f$? After all the notation $f(x)$ existed since Bernoulli ~1718. Didn't they also call $f$ a function? No, not officially. The first ones (Bernoulli, Euler, Lagrange) called $f$ the characteristic of the function $f(x)$. I interpret this as saying: its just a character used to distinguish one function of $x$, say $f(x)$, from another, say $g(x)$. But mainly people before 1900 didn't call $f$ anything at all! Peano for example doesn't in his calculus book. In fact, no one treated $f$ as a mathematical object on its own, before Dedekind, Peano, Cantor and Frege (to a certain extent independently) changed that around 1890. (There are some surprising historical bits in that thread. For example: Dedekind, Peano and Cantor all gave $f$ a new name, calling it resp. "map", "prefix sign for a function" and "allocation". They all preserved the original use of "function" for $f(x)$! Moreover Dedekind formulated his notion of map nine years before realising that he could identify it with the $f$ appearing in their functions $f(x)$. Only Frege (unfortunately) suggested calling $f$ a function, and somehow it became standard. We would probably have less difficulty communicating today, if $f$ had not gotten the name function.)
Returning to $y=y(x)$ and why Jacobi started that. Besides the good reasons about partial derivatives he gives in De Determinantibus 1840, I suspect that he simply wanted a notation to indicate of what a certain variable is to be considered a function. I used to believe that in the equation $y=y(x)$ the $y$ on the left and on the right were objects of different types which by abuse where given the same name (the right one being of type $\mathbb{R}\to\mathbb{R}$, the left one of type $\mathbb{R}$.) But I now think that this is not what Jacobi intended and how physicist would like to use it. Instead, we should literally think of the $y$ on the right and left as the same object (of type "variable quantity"), and what is being abused is the notation for function application $f(x)$. In other words: had Jacobi chosen another notation like square brackets $y[x]$ to annotate that $y$ is considered as function of $x$, instead of using the already existing notation $f(x)$ for "application of a map to a variable", we might have less trouble with it now. I suspect one could formalise this idea similarly to how computer scientist formalise "ascription". See for example Pierce, Types and Programming Languages.
Having said that, I don't think that by doing that we would gain much. Writing $\mathbf{r}=\mathbf{r}[t]$ seems mainly an aide for the reader, and we might as well do without it, as mweiss suggested. The harder problem seems to be to correctly formalise the notion of "variable quantity" and surrounding things like the notation $dy/dx$.