"As the second partition fills up with "one a month" back-ups of ghost images, and document back-up. Would the performance of the primary partition be affected during projects? "
No, it should have no effect. Fragmentation and related issues are the only real performance cost of a drive filling up, and the separate partition mitigates that. Head travel isn't an issue because you're not doing the backup or otherwise using it while you do your audio work.
Could be worth considering an external backup for other reasons though, but that's not directly related.