As of 9.0.0.3, all special characters should be handled when sourcing from OBI and deploying to OBI using linux endpoints and with FlexDeploy running on Linux.
On Windows, folders and files cannot start or end with spaces, but this can be done in OBI. If it is done, Windows endpoints cannot be used, and FlexDeploy on Windows will have similar issues.
If you are exporting to SCM, most special characters should still work on Linux, but more failures on Windows are likely. Windows has protected names for files and folders like COM2 and CON. If you use a protected name as a folder name in OBI, this will also fail on Windows. Git SCM is tested the most with special characters. It is likely that other SCMs will have issues handling special characters.
You can open a support ticket if you find an issue with special characters or have any other issues.