I play using my HDTV as a monitor, so I'm six or seven feet away from the screen. Everything in Spiral Knights is perfectly legible *except* for the tiny quantities on materials. It's worst on the tokens, which all have very busy icons underneath the white number.
It'd be great to have the quantity pop up on the mouseover tooltip. It looks like there's room to put it up on the title bar for all but the longest of names, or maybe in a bubble popping off the lower-left corner where the white border says "material" or "token". As long as the text is as big as the star-damage numbers I'd be able to read it.
I'm fine reading them, and I don't play on a huge screen. Just sit a tiny bit closer if it's bothering you.