The Snowball Effect SK plugin uses it, for example, to reward regular,
previously-approved commenters with good karma, so you might lose that
benefit if you delete the entries. Perhaps you could delete
everything except the last couple of weeks' worth of entries to keep
some benefit for recent commenters.
But no matter what, in my opinion there's no great loss if you clear
out the table.
We really should look into more efficient ways of storing data, as
wp_sk2_spams does it about as inefficiently as possible.