Submarines rarely got "into" carrier fleets during air operations. What usually happened was that damaged carriers were happened upon by opportunistic submarines. In situations where fleets were moving at tactical speeds, submarines hadn't a hope of catching them, but coming in and out of port, or on random transit, that's where the subs really made their money.
This is one that is harder to quantify as well, since stat summaries rarely distinguish between a sub getting a kill on a damaged ship or straggler vs picking something off from an operational task force. Both things happened though.