I'm not sure there are 'hundreds' of them to begin with, and there are definitely not hundreds of them running right now. I just did a week on the Smiling Seahorse, going from Koh Lipe in the south to Richelieu Rock in the north, and didn't see more than one or two other boats at any given location. MV Lapat (
Similan Seven Sea Club – Padi 5 Star Dive Resort ) was operating, as well as Sea Star Andaman (
SeaStar Andaman – Happy Journey ).
Me, having done a trip on the Smiling Seahorse in March last year, I'm not even considering any other boats anymore - I've done three more trips with them this season (one in November, another in December, just came back from the third in January and heading out for a fourth tomorrow). They're a bit on the pricier side, but since the owner is a photography enthusiast and the boat is custom-built, there is a large and well-appointed camera room, and they're the only operator in Thailand that I know of who run blackwater dives on a regular basis - at least one every trip, more when there's interest and opportunity (best area for blackwater is Koh Bon/Koh Tachai, and it needs reasonably calm weather); last trip we had two blackwater dives. If you're not familiar with blackwater, here are some shots from the last trip:
Don't make solid plans too far in advance as conditions are fluid and changing constantly. Thai government regulations change on a whim, liveaboards can easily cancel trips on account of not having enough customers, airlines may move flights, etc.