The simple answer is as Hawk and Sam say - its one 'hit'...
The more 'buried' answer... is the POTCO code - the 'combo' attack of a weapon is totalled to be considered one 'combo hit' (when the combos appear for example: 11 Hits 1963 Total - is the total of the entire hit, and not counted as seperate hits).
As for benifits of REPS and swings - sometimes it is, sometimes it isn't - worth it. For example, questing items tend to ask for a lot of 'Get 5 of X' where its actually faster to just get the 5 then get the 500 REP for them then to try to 'hack' at the 5 for a few extra REP. Much later in the game when you are after enemies with semi-much higher levels and its your only focus - then take your time and get the extra REP for the extra hits.
In the end - its all about play style I think - as long as I'm having fun now thats all I focus on (otherwise I should have had three Mastered Pirates by now
)