Does an exclude mask prevent a matching file on the remote server from being deleted?

If I have an exclude filemask on a synchronize command and a file with that name exists on the remote server, does the remote file get deleted?

No it won't get deleted.

It's not documented specifically for the scripting command. But in general for synchronization, see:
https://winscp.net/eng/docs/ui_synchronize#file_mask