Well probably only if you align with someone. Which yeah, I doubt a faction would let you spy for them unless you were aligned with them or at least friendly.Powerplay is slated to change that, at least between Power factions that are in mutual conflict.
Maybe have it so you have to scan a system for a secret base like what was said above. When you get close to a planet RNGesus picked a USS like marker appears (but maybe called something else like Encrypted Signal or something) Then silent mode scanning and maybe sample collections. This could actually be really fun if done right. The setting is also important like a Capital ship under secret construction behind enemy lines.