1. The hole is no big deal. You can probably use it to run the string from another type of extension, or if you don't use one, just ignore it. If it really annoys you, plug it and varnish it over.
2 + 3 - Hard to say for sure, but adding a different extension probably won't cost any more than installing that extension would on a bass that had none to begin with.
All that said, I'd keep the mechanical and fix it. Just 'cuz.
