They do count crossovers. There's some leeway for situations like, say, HDM, where a ton of fusion fic for other fandoms gets tagged with the fandom tag for HDM, but I think the mods have said they will no longer consider evidence posts for fandoms that are over 1,100 qualifying works between AO3 and ff.net.

Agent Carter has 2721 Yuletide-qualifying works on AO3 alone, so I don't think the Yuletide mods would consider that.

For what it's worth, Peggy/Angie is in under MCU for Femslashex, along with a bunch of other Agent Carter ships!