I found out why it doesn't work (sorry, but this is now very technical):
The on-demand files in Onedrive are implemented using reparse points. That's also why NTFS is required and Onedrive won't work with FAT32 or other file systems.
Problem is, most applications don't work properly with reparse points, so Onedrive also implements a file system filter which makes sure that applications won't even see the reparse points but only normal files. But here's the big problem: the file system filter is deactivated for the explorer process!
You can test this yourself if you open e.g. notepad and open the file-open dialog: there you can right-click and the TSVN menu shows up properly. Only in Explorer the menu doesn't show.
And since the file system filter is a driver, I can't work around this.
The only way to get the context menu working for Onedrive folders is to actually handle the reparse points in the svn library. While trying to figure out the problem I also checked the svn library code and to make everything work properly with reparse points is not quite easy. Especially since to test this, you have to use a shell extension - as I said all other apps/processes 'see' the real files due to the file system filter.
For example, the TSVN dialogs all work properly if you start them manually, e.g.
TortoiseProc.exe /command:repostatus /path:"d:\Onedrive\svnproject"
will work just fine.
One more thing: while I could get the context menu to work eventually, the overlay icons would never work: Onedrive has it's own view implemented in Explorer, and that view does not show overlay icons from other shell extensions. So those will never work.
Sorry for the bad news.
Stefan