The original manuscript has the present-tense are, which Oliver Cowdery copied as were into the printer’s manuscript. Nonetheless, the whole sentence is in the present tense; the are is consistent with the preceding present-tense suppose. The present-tense are provides an immediacy to the historical account here.
Summary: Restore the original present-tense are in Alma 63:8 (“they are drowned up in the depths of the sea”); this use of the present tense is consistent with the preceding present-tense suppose.