Since the hatches are mechanically fastened - either screwed into the deck of clamped between an inside and outside frame - butyl tape is a good choice for sealing. Here is a link to Bed It Butyl Tape which is recommended by Mainesail
When I reset the forward hatch and replaced the lewmar ports I put the tape on the inside lip of the hatch frame, tightened the screws to compress the butyl and squeeze some out around the perimeter. After letting it sit for a day or two I tightened the screws where needed and cleanup up the excess. Since it isn't an adhesive cleanup is easy.
I use the butyl tape for almost everything going through the deck, it works great, can be removed if needed and cleans up well. 
If you search Mainesail and Butyl Tape you'll find several articles.
 

Rich -
While we use Mainsail's "Bed-it" butyl tape for lots of stuff on our boat and think its great stuff, we were unsuccessful with rebedding our overhead hatches on our current boat (a CM440)  with butyl -- they still leaked  (note that the hatches were originally bedded at the factory with butyl -- a lot of work to clean it off for rebedding!).    A friend on a Benetau had similar issues with butyl, and said that one he redid with 4200 leaks disappeared.     So we redid the rebedding job  -- this time with 4200.  Et Voila! -- no more leaks.    4200 can be a lot messier to deal with, as I'm sure you know, but if you mask the area well with tape before applying you can get a neat job.