"While" and "and" perform the same function grammatically, the real separator would be a semi-colon. Otherwise the sentence does seem redundant, but that is the way it is structured. Any other assumptions are merely those of the reader.
*shrug* You might be right on 'while' and 'and,' I don't know. Personally I think they have somewhat different connotations, anyway. Either way, the sentence doesn't say that battleships are only better against small craft and missiles, nor does it suggest that they can only absorb tremendous amounts of damage from missiles and small craft, but rather that they can absorb tremendous amounts of damage, with no qualifiers. The sentence structure suggests that these are the two advantages of battleships: that their secondary batteries make them virtually immune to missiles and small craft, and that they can absorb tremendous amounts of damage. I fail to see how the sentence suggests that their ability to absorb damage only applies to missiles and small craft.