Working out players is indeed part of the "scouting" process. It lets you confirm with your own eyes a few things that it might be hard to judge with tape alone. That's pretty routine and accepted, I would think.
Just because you have a guy on your draft board, doesn't meant that you are "targetting" that player.
For example in the 2008 draft if I'm the San Diego Chargers, I would have McFadden on my 1st round draft board, but since I have LT, that doesn't mean I am TARGETTING McFadden or even thinking about drafting a RB. See what I mean? Proof of a guy being on a team's "draft board" in a certain round is no proof at all that the team is even interested in drafting that player. It is only proof that the team considers that player talented enough to be on the board in such and such a round.
The Patriots obviously considered Vilma a 1st round talent. But they didn't draft him and as far as I know they didn't attempt to move up to draft him. That tells you something bit about their priorities and draft philosophy.
If the Patriots finally draft a 1st round linebacker, I'll be the first to congratulate you, because it doesn't fit the pattern of Piolichick's drafting so far at all.