Some of the boats I have been on seem to have somewhat of a Don't Ask, Don't Tell policy. If you actually ask if you can dive solo, they probably will say no unless you have a Solo card. But, if you don't ask, then somewhere along the way they will ask everyone if they have a buddy. If you just, basically, give some sort of grunt or nod or say "I'm all set" they won't "know" (or care!) that you're diving solo.
On those same boats, it's completely normal that people drop in and meet their buddy down on the anchor line. So, buddies don't necessarily waddle up to the entry together or pair up on the surface. So, if you don't tell them you're solo, they probably won't ask and they won't really have any way of knowing for sure. Which seems to be really what they want - the ability to say "we thought he had a buddy."