A player with a light touch can make nines sound fine. I just don't happen to have a light touch at all. For me, many notes spank on the fingerboard.

The biggest reason IMO is that niners make a guitar feel so slick in the store.... "wow! it's so EASY to finger!"

If you change gauge the nut and/or bridge may need some attention.

When I bought a new Fender Toronado about a year ago the nut was cut so precisely for 9-42s that it needed work to accept 10-46s. New Strats and Teles I have bought since then weren't slotted quite as precisely and the string gauge change was not a problem nut-wise.

You are right about the trem springs and such being a part of why a gauge change requires major setup work on a Strat. Nevertheless any time string gauge is changed the intonation should be checked and probably fine-tuned even on a hardtail.
Doctor, I have a constant ringing in my right ear.