Sure, just add them to exclude file mask:
https://winscp.net/eng/docs/ui_transfer_custom
https://winscp.net/eng/docs/file_mask

Hello,

I sync several image folders (and a few other items) from a folder that a Mac also syncs to/from and it always drops the .DS_Store file into that directory. Is there a mechanism from winscp to block all .ds_store files from ever being sync'd ? The reason I ask is that there is a problem with .DS_Store files, in that if they end up online, they can be read by the public for file structure, etc).

I use WinSCP all the time, and this would be a very useful option.