I'm using version 1.8.8 (compiled by myself for Debian Wheezy) and, even though the "Mark as read" entry is present in the context menu for the search folders, it doesn't seem to work.
Thanks for your attention.
Reproduced. This should be fixed.
As a workaround you can use "Mark All Read" from the context menu of the search folder in the feed list.
Fixed with new release 1.8.10. Please retest!