The largest, and most obvious issue with suction as a way to control boundary layer is that the holes traditionally used for that are likely to plug quite rapidly in the salt environment.
IIRC the navy tried it in the late 50s or early 60s, and they had the same issue, even with the maintenance schedule they had for experimental aircraft (read as S***LOADS) they couldn't maintain the system on one aircraft to where they could rely on it (done for low speed handling improvements, so having it not work, and not be able to tell, untill the aircraft stalls on one side, at too high a speed).
Or at least that's what I read about it.
There was a company at one poit in time that was selling titanium leading edges for select Cessna wings (I haven't heard of them since the "recession") that were laser drilled for the same effect (came complete with an STC, and a large vacuum pump).
I've only seen one of these systems in person, but the owner, and all others I've heard from say the bane of them is they get packed full of bugs, and are a PITA to clean out.
I've mentioned the same issue several times in a row as any of the cars on the salt hhave a coating of salt on any area with a negative pressure, even after only one pass,
I personally have no issue with cleaning the car after each pass, but it would be dificult to get small holes to clean in a timely maner, and large holes would be difficult to supply with enough flow to generate the necessary boundry layer reduction.
If you have a suggestion as to how to avoid that issue, or clean the systems out faster I would love to hear it.