I did some testing last night against the Moskva and admiral Kuznetsov, and it seems to me that for as long as you stay below 10ish metres your biggest worry is CIWS. And by this I mean that you are completely immune against missiles. I was unable to provoke a missile launch when flying at this altitude. Already launched missiles would self destruct when I made the descent to 5m. I don't know how realistic this is, or what IR SAMs will do.
5m or so is (in dcs) sufficient altitude to launch rb-05 and rb-75, though the latter is usually shot down by SAM due to the high trajectory.
The rb-05 is surprisingly easy to guide into the waterline of a ship when flying on the deck. This basically makes it a torpedo. However scoring two direct hits on the Moskva did only 0 and then 7 % damage.
Beaming with countermeasures is also very effective, albeit a bit riskier. Not so effective against multiple ships either.
Running away is always an alternative. A clean viggen is not easily caught by a SAM if it has a decent head start.
I ended last night experimenting with toss bombing, but I couldn't get it to work properly. The bombs would always fall long. If you can get it to work that might be an alternative in the anti-shipping role, in a "We're out of guided munitions scenario".