The scores are calculated in ATB (Auto Team Balance) http://www.ut-files.com/index.php?dir=ServerSide_Mods/AutoTeamBalance/&file=AutoTeamBalance-1.5_HighScores_release.zip
It's configured on the server to use scoringmethod 0 which means it is based on total score in game. Score this way includes frags, grabs, caps, flagkills etc. based on the values for each set within SmartCTF.
It does get slightly more complicated within ATB because there is some relative normalization and some weighting toward the current game performance versus historical scores. After 4 months, IIRC, old scores are completely forgotten for a player within ATB.
Anyway, that is the high level overview of how the scores are calculated. If you check out the .jpp file in the ATB archive you can read the code and get a much more specific answer if you are inclined to do so. 🙂