Cebu is a shipping hub. There is a lot of maritime activity going on. Cebu-based companies control most of the country's shipping. Shipping schedules are published regularly in the newspapers, but, at this point in time, the Wa'y Blima! Shipping Guide seems to be the only searchable online database of shipping schedules.
Now, before planning your excursion, be sure to contact the shipping line directly and confirm the sailing times of your boat. Schedules may be changed or suspended without notice. For instance, vessels may be dry-docked, and there's always the possibility of a strike. Earlier this year - 2004 - Sulpicio Lines was bogged down in a strike and all vessels were berthed for a while. (Sulpicio made a pretty strong comeback however, by launching the biggest passenger vessel in the country, Princess of the Stars, a few months later.)
Also note that boats get pretty crowded during major holidays: Easter, All Saints Day and All Souls Day (November 1 & 2), and Christmas. You may have to fight for seats at these times.
Safety standards on the Philippine seas are good. The Philippines - especially Cebu - continues to train seamen who man vessels for major shipping companies all over the world. The Philippines has had one disaster in recent memory; ironically it was a large and modern WG&A Superferry that suffered an engine room explosion in 2004, resulting in the death of a quite a few passengers. In general, however, maritime travel in the Philippines is safe. You won't find boats overcrowded like Bangladeshi river ferries. The main problem is, in the case of some shipping lines, out-dated equipment; occasionally old engines conk out and the Coast Guard has to be sent out to rescue the stranded passengers and crew.