The thing is, covert ops can't "send a message." It runs entirely counter to the idea of being covert.
That's why I'm skeptical the nerds could really be operating some giant conspiracy; it doesn't seem to get them much. If they aren't taking credit for it, then the objective must be to keep other factions distracted. But to what end? I'm sure they would love it if the other frats would ignore them and focus on each other... but they were already doing that! The only thing we know either of the frats have done to the nerds so far is for the maggot brothers to give one nerd a wedgie. Surely that's as close to 0 as ambient threats will ever get. Trying to stir up trouble between the other frats seems just as likely to get them caught in the crossfire as it does to improve matters. And that's assuming they don't get caught; if they do, things get much, much worse.
The idea they are trying to get their hands on the DIK mansion is a more interesting motivation, but again I don't see how this would accomplish that. Unless we believe real estate in the vicinity of B&R is so scarce as to be priceless, their problem seems to be one of funding not opportunity. Even if they trash the mansion to the point it's dirt cheap to buy, all that would do is force the DIKS to have it renovated. I mean, unless they knew Rusty's dad was close to cutting him off, surely that would be the expected outcome of their vandalism. Rusty's bought his way out of everything else, why would he stop now? Even if the nerds did know he was maxed out (or assumed Rusty would just buy a new one), they'd still be left with the fact the place is trashed. If the DIKs couldn't afford to rebuild, what would make the nerds think they could?
I'm willing to accept that the nerds might be up to something, but the mansion job just seems like an inordinate effort to go through for such a nebulous gain. I could believe, for example, that someone paid the nerds to pull off the Cathy cluck, because the nerds could plausibly be one of the few groups with the skills needed to pull such a thing off and money is a useful resource. But I can't see any reason for nerds to trash the mansion.