It just occurred to me that another way to look at the question is by analogy to magic items. Rings, hats, cloaks, boots, etc. (both magical and otherwise) are far more fragile than the PCs who wear them, but in 3rd Edition, failing a save vs. Fireball doesn't mean they're all in danger of destruction (unlike 1st edition... ah, happy memories ). By RAW, the worst that can happen is, if you roll a 1 on a save, *one* of your items is in danger.
So, if you want to houserule that Fireballs can destroy eyestalks, each eyestalk should get a save, *and* the same risk should apply to PC's gear. Or, you could houserule that Beholder eyestalks are like magic items, so if the Beholder rolls a 1 on a save, *one* of them might be destroyed (see Spell Descriptions :: d20srd.org). This might also imply that the eyestalks are subject to being attacked as worn items.
So, if you want to houserule that Fireballs can destroy eyestalks, each eyestalk should get a save, *and* the same risk should apply to PC's gear. Or, you could houserule that Beholder eyestalks are like magic items, so if the Beholder rolls a 1 on a save, *one* of them might be destroyed (see Spell Descriptions :: d20srd.org). This might also imply that the eyestalks are subject to being attacked as worn items.