No, the line endings of the input files don't matter. Tested with a C and SQL file (random choice) with LF and then again with CRLF line endings and the generated tags are the same.
I don't get it. Basically when you take the SQL tests that fail with CRLF line endings and open them in Geany, I would assume that there will be tags missing in the sidebar.
With the binary mode change we would also alte rthe behavior when writing tags files which then always contain only LF. I think this is fine even on Windows.
In fact, since we are considering 2.0 release and making "breaking" changes, I was thinking we could switch to the ctags tag file format for tag file generation, unit tests and the tag files we ship. We could still keep support for reading the "proprietary" binary format we use now but using a more standard text format would be nicer IMO.