First of all, it's illegal. Believe me, they know where you've been. I say that based on a "former life". Sure, they may be busy and let you slide, but then again...
The assumption is that if you don't check in, you must have something to hide. Checking in is very easy. We've done the "local boater" option in Fl, but usually go to Charleston from the Bahamas and they come to the boat in less than 30 minutes...very easy process.