The NCAA rule on this is enforced infrequently, and whom they choose to target/how they decide who slides and who gets attacked is a mystery. Search Andrew Oliver on this site to read about his saga. It really only comes up for the guy who ends up not signing in the particular draft.
Since the adoption of the new CBA a few years ago, the value of an advisor-cum-agent can be fairly debated. You're not going to get much if anything more with one than without one, so giving away a percentage of your bonus to one as a fee is not the greatest idea. Especially since the signing bonus is about all the money anyone ever sees unless and until they get on the MLB 40-man roster.
If I had a son deemed likely to go in the first round, I would think I'd want an advisor to make sure we knew what we were doing, what we were signing, and what things may or may not actually be negotiable. Since bonuses can drop off precipitously as the draft progresses, though, there aren't really that many guys I would expect would benefit from an advisor. I've even known some scouts who've given up this whole aspect of their business model, because there's just no money in it for them any more.