Peter's probably the best person to answer this, but yes - it collects statistics for every song played, shuffle mode or otherwise. There are multiple shuffle types in 1.1, the default ISTR is least recently played - so yes, if you play an album directly, it's likely to end up near the end of an all-player (or even all-tracks-by-that-artist) playlist.

It keep stats on skipped tunes, though I don't think anything is done with that yet.

Hugo