I think that qualities - negative or positive - should be in some manner important. Tough as Nails is easily a very useful quality...unless the character is a "stays out of the front lines" hacker, when I'd recommend they take Codeslinger or something else instead so they get good bang for the karma. One of my games had my players strike a Triad watch post and one of the pieces of loot they nabbed was a gold sustaining focus. Caster's allergic to cold, so he sold it. Sure, maybe it's skirting the allergy, but I didn't have a problem with it. The character might have done it minus any metagaming reason, even without the player knowing "I have gold allergy on my character sheet".
... "I have gold allergy on my character sheet" translates to "my character has, in the past, had an allergic response to gold". It is not metagaming to have your character avoid their allergens.
What annoys the fuck out of me here is that gold is Hypoallergenic. *Nobody* is allergic to gold. (Though they can be allergic to additives.)
Magic makes science go play while the grownups talk? J/K, but seriously, given three rounds of VITAS (the A stands for Allergic, IIRC), and things like elves, trolls and vampires running around, what might once have not caused allergies may interact badly with some people because, well, magic is screwy like that.