There are two different things to consider, imo.

Firstly, in a PUG, I'd have each toon roll on anything that was an up for the toon in question.
If you have four toons, yet only one is upgraded, only that toon should roll.
If you have four toons, all of whom are upgraded, they should each roll.

Secondly, in a guild run, it really comes down to how often your secondary/slaves will attend.
If they are there as fill in characters, the secondaries probably shouldn't roll against a main.
If on the other hand, your team will attent the majority of raids, they should be treated as individuals.
If the guild wants to give you a single dkp pool, that's fine, but then each toon should earn dkp simultaneously.
Bottom line: If the team is part of the progression, they should gear up too.

I've personally, in the past, been told only one toon can roll, and have in those situations only brought one toon.
Pretty much, if I raid, its 1-boxing now.