Make sure you actually added /home/yourusername/.vst3 to REAPER's plugin search path, where yourusername is your username on your Linux install. Please just use the GUI to add the directory so you can't make a typo. If you really added /.vst3 to that search path like you said, then REAPER would not be able to find the plugins.
Secondly, don't add ~/.wine/drive_c/Program Files/Common Files/VST3 to REAPER's plugin search path. That will cause the plugins to get blacklisted because REAPER's plugin search is a bit buggy and it will blacklist plugins based on their name, not on their path. So if REAPER finds the Windows VST3 plugin during the search (which it obviously can't load), then it will consider any plugin with the same name blacklisted.
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