Just happened to check the Atlas Game sites's FAQ and found out that the points count for the guests after they're killed.
From the FAQ:
Q: Let say you have Whiskers (from Unwelcome Guests), who is worth +5 in category base. If the cat gets killed and is flipped over are those points then gone? So its modifiers would be the only thing that count?
The base points DO count. Technically, it would have made the most sense to have the guests printed with scores on both sides to address this, but the clear plastic makes this impossible. As it is, simply don't flip guests if their scores are showing.