Yes, I found it particularly annoying when I was first starting out and not particularly good at combat. I jump to SC to get my shields back, after knocking my target down to around 54% and I would be at 70% after escaping. Find my target again in 2 minutes or so, thinking I'll finish him off and he is fully repaired and I'm stuck at 70%. It's not very easy going at the point in the game.
Well don't run away then.
Limitation of current system.
Have you reported this in the bug reports sub forum? I would if I were you, it does annoy the heck out of me, when I stay damaged, but they magically repair when I interdict them again.
That's a limitation currently - the spawn in super cruise is simply entirely new (will often have new wing mates too).
I've heard that will change though.
This Is not always the case, in my experience.
Ive been interdicted by NPCs, done some hull damage to them until my FSD came back up, then went back into SC only to have the same NPC follow me. The value/states of hull/shield stayed persistent.
The values are suppose to stay persistent nowadays. This was added somewhat recently, so I would send in a bug report.