I think a partial solution to the cluttering exists in the game already.

As you can already 'affect target, special', and have a specific group of affects listed under the relevant heading, it might be interesting to have a "quest affect - applied" under normal "affects", and typing "affect, quests" would expand the list to its entirety.

Even if item affects were grouped together, the problem of decipherability would remain. Example:

item affect - strength +8
- hit +6
- damage +6
- hit +5
- strength +12
- physical resistance 10%
- fire invulnerability 5%

With multiple set bonuses/special item affects active, it gets far too difficult to decipher what's doing what (just as it is now on a player's quest affects if s/he has a Sigil Citadel stat bonus, an eldritch cordon set bonus, a Misty Tower page quest, and a Golden/Dark age boost active).

I'll have some solution in place by the time I start introducing such items. =)