Deleting file bytes

Have a way to delete bytes of a file opened with FileOpen without deleting the file and re-writing all bytes of a file again?

If all of the bytes are from the end of the file you can call SetEndOfFile using the System plug-in, else you'd have to read and rewrite unless someone can think of a better solution.

Is this planned for a future version of NSIS?

No. You already have what you need to do this.