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Good question. With ePO 8.6.1 on a VSE 8.0i or 8.5i On-Access Default Processes Policy, the exclusion window states:
"What to exclude" followed by a check box stating "Also exclude subfolders"
The word "Also" leads me to believe that if you want the subfolders excluded then you would have to check the box.
I suppose you could also manually type in a pattern which would exclude subfolders, but the wildcards and rules for this is fairly confusing (at least to me). Check out KB50998 for more info.