Are cap staples eventually visible under asphalt roof shingles?
Probably. I wouldn't do that. Modern fiberglass shingles are fairly thin compared to the organic (paper) mat ones of the old days, and you will likely see the bulges after a few hot days. 

The manufacturer probably only recommends using cap staples under the assumption that it will sit exposed for some period of time and needs to hold up to the wind. It's completely pointless otherwise, as a million shingle nails eventually hold it down anyway.