Of course, if you write x(3), other mathematicians should frown at you because you're making bad notational choices.
It's a bit like explaining to students that the real way to know which 3rd declension nouns are i-stems in Latin is to say the genitive plural both ways. The one that doesn't sound wrong is correct. But you have to have a lot of time in the language for that to work.
edit: I suppose, what I'm trying to get at, perhaps too glibly, is that audience matters terribly much in mathematical writing. In the same way that Latin students don't start with Tacitus or Sallust, famous for their idiosyncratic grammar, math students shouldn't jump into the full context-dependent mess of the notation that experienced mathematicians use.
But I think we often thrown them in unintentionally because we're so used to it.
Btw, I wouldn't abuse latin comparisons on an american forum, I don't think it's quite in the culture ^^
Of course context would help resolve this if you have a function named x or not, or a variable named x or not, and if you have both a function and a variable named x, well, you worked for your confusion and you have obtained it; congratulations. :)
However, the notation is relatively clear notwithstanding. It almost has to be x as a function with an input of 3.
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.
But I get your point.
I have also heard the objection that [x] is a 1×1 matrix whose only element is ‘x’.
(I have no mathematics background past K-12)