Yes, but where once not that long ago the only teams running the 3-4 were New England and Pittsburgh, we could now see up to eight teams running it:
Denver
New England
San Diego
NYJ
Cleveland
KC
Miami
Baltimore
Given the lack of 3-4 teams in college, that will really put a strain on the number of players available to step into the sytem quickly, and will leave a lot of teams, the Patriots included, looking at long-term conversion projects a la Tedy Bruschi. It will also likely mean a lot more competition for the 'right' free agents. Guys like Dansby and Scott will be happy with the extra bidders, but the Patriots' salary structure will likely be tested.
First, the Chiefs probably won't switch to a 3-4 until next year at the earliest since it looks Herm is coming back. Besides, they spend some high draft picks in recent years trying to get 4-3 players. Pioli might decide it may be better to build a 4-3 team especially if he hires a head coach with that philosophy.
Second, the Jets could switch back to a 4-3 now that Mangini is gone. Rex Ryan loves his father's 4-6 and if he gets the job, he may move the Jets to that formation once he has final say over all philosophies. He pushed for it to be implemented under Billick.
Third, with Ron Rivera as the DC of the Chargers, he might morph that team into a Tampa 2 defense. That is what he ran in Chicago and it was a dominant defense. So the Chargers could let go of some of their 3-4 players in the next few years. Granted they are an one gap 3-4 defense which is very different than the Pats' two-gap.
Fourth, Baltimore could change their defense after this season. If they lose Ryan and two of the three free agent LBs in Suggs, Scott, and Lewis; they may decide to move back to a more traditional 4-3.
So there is a chance that there could be 3-4 less teams running the 3-4 than you state.
Besides, there are two sides of every argument. With more teams running the 3-4, it also means that there will be far more free agent LBs in near future who will be versed in the 3-4 and can come into the Pats and make an immediate impact. The chances of the Pats acquiring Vrabel type of players increase in this scenario. There will be LBs who aren't seeing playing time because of depth at a certain LB spot who can come to the Patriots and potentially break out right away because they already know the Pats' system.
I don't think it is as dire as you make it sound. The Pats have rarely drafted a LB who has made the team anyway. In fact, it wasn't until the 3-4 became all the rage in the NFL that the Pats even drafted a LB higher than the fifth round. So if a couple more teams start running the 3-4, it isn't going to affect the Patriots drafting? San Deigo and Pittsburgh have never been active in free agency and choose to draft talent instead. The Jets are going to be cash strapped for the next year or two. So is Cleveland. Neither will be big free agent players.