I have a different phone, and have issues also with the media applications ignoring the .nomedia flag.
A web search indicated that the .nomedia flag is not working as expected because of a Cache. (the previously scanned data remians in said cache)
Renaming the folder, then re-scanning the media seems to fix this issue with the cache holding the data even after the .nomedia item is present. After scanning, the folder can then be renamed back, and additional media scans seem to properly ignore the folder.
I am not sure if this is a long term workaround, or just another bad workaround, but so far it has solutioned it for me on my device.
Update, renaming and rescanning the media has worked 100% for month now, only if a new set of items are scanned prior to the .nomedia flag being placed in its folder, do i have to apply that method again. So .nomedia goes on first :-) . I see many programs are tossing the flag in early , even if thier folder is empty at the moment.