There were some Abe Sapien stories in the first Plague of Frog collections which were the "un-numbered" Drums of the Dead and a backup in a Hellboy book.
I've been working off the (excellent) Hellboy Wiki here http://hellboy.wikia.com/wiki/Abe_Sapien_(series) from the "Numbering" section, there are 10 issues before the ongoing starts which havn't been collected in any of the Plague of Frogs volumes (I currently have 7 of those 10 I think).
The paperbacks did infact call the first ongoing issues Volume 3 so their could be a good chance of these mini's making there way into the hardcovers. I guess I'll have to wait until the official solicitations to find out.