I don't know how much an issue they are for new players. I think for most pros, it's not a matter of them being easy experience - they're just annoying to deal with. The vets want to fight each other directly, through a battle of production, micro, and strategic positioning, without dealing with outbidding each other for the pirates, or dealing with periodic pirate raids. Thus, I doubt this would have any effect on them being off for pros games.
100% agreed, its not their difficulty that makes MP regulars turn them off, its their annoying factor. Same reason the regulars don't generally play with Ai in the game, and much prefer there not be. I have played a couple of games MP on diplomacy that we took advantage of a lot of features and they were certainly a load of fun. I played a 1v1 with another guys the other day where we unlocked teams and added 2 Ai so we could play around with the diplomatic aspect of the game. I ended up winning by being more diplomatic with the Ai, having them harass my opponent while I built up a massive econ, got sweet pacts and built a huge fleet. Was a great game.
Mp regulars are still going to play team games, but with all the new blood coming to the game, its not hard to get some ffas going.