The best reason not to run a 2NC counterplan against an experienced and well-researched affirmative team is that they'll straight-turn it several ways, leave the 2NR with a whole lot to cover, and then go deep in the 2AR on whichever argument the 2NR did the weakest job answering. I think the theoretical objections to 2NC counterplans are an uphill fight to win in a debate between evenly matched teams, but the substantive strategic risks they pose for the negative are the real reason you don't see more of them.
Dangit, he took exactly what I was going to say. Well, mostly.
I'm fine with them from a theoretical standpoint. A constructive is a constructive, so do whatever you want with it. I know I'm much less of a traditionalist than most of the NCFCA community, but I don't care one bit about running or not running strats because of "fairness," "education," or "ground." If its unfair, then the aff can run that argument and win that its abusive. I don't think there's a such thing as in-round education loss, and, to quote a fantastic debater who graduated in 2012, "Ground is what you walk on to go to the library and do research." So, from a theoretical standpoint, knock yourself out.
From a strategic standpoint, probably not a good idea, even if you run it conditionally or dispensationally:
You would think that if you run it cond/dispo, then the 2NR can kick it quickly and go for something else. Problem is, if the aff runs cond/dispo bad in the 1AR, the 2NR won't have a good time. Any good aff will realize that and run a quick, 1 minute shell they can collapse to if its undercovered. That forces the 2NR to spend probably 1-1:30 on it, which is pure defense (therefore with the aim of "don't lose," rather than "win"), leaving very little time to actually try to win the round. So you're in a bad position if you run it dispo/cond. In an outround once I was neg and ran two Ts, dispo K, DA, and case answers. My opponent ran a dispo-bad shell that sucked her time, but she knew I was probably going to kick the K. So even though she spread herself out, she forced me to answer dispo bad. That spread me out even more than it spread her out, and forced me, in terms of time allocation, go for everything. In other words, even though I kicked the Ts and K, I spent so much time kicking the K I spent the same amount of time kicking it as I would have going for it (from a theoretical standpoint, I couldn't just go for it and say I didn't violate the dispo-bad because the in-round abuse she was claiming occurred the second I said "dispo" in CX; even though I eventually would make it my advocacy, it still skewed her 1AR strat, which was the abuse). I lost on a 2-1 exactly for that reason. Granted, that was LD, but the same concept applies.
If you run it as unconditionally, then any good aff will just throw out 6 turns, answer back case, extend the turn you inevitably drop, and win on a risk of solvency.
So, from a strategic standpoint, I would say no.