It depends on the context. As an intermediate step I definitely write things like x (3) meaning multiplication, as it can more clearly indicate what's just happened (see my other comment in this thread).

There's other context too, based on what is known. Up to a certain point in first year at my university, most engineering students haven't ever seen functions named x and y, and so they'd mostly interpret x(3) as multiplication. Then we show them parametric curves, and suddenly x(3) looks like the x coordinate of a point on the (x(t), y(t)) curve.

This is one of the reasons I annoy people by following Wolfram’s convention in Mathematica of using square braces to denote arguments passed to a function: f(x)=fx=f×x while f[x] means “apply the function f to the argument x”. An unusual convention it may well be, but at least it’s one devoid of ambiguity.

It's not devoid of ambiguity, because f[A] usually means the image of the set A under f.

Not at all. f[x] is clearly the xth component of the array f :-D

On the blackboard in the mathematics department it’s not.

But I get your point.

I have also heard the objection that [x] is a 1×1 matrix whose only element is ‘x’.

Square brackets can also denote the floor function (especially in old works where '⌊' and '⌋' were typographically unavailable).

An array is merely a function from N to some set.