You don't have anything to spend money on till you get back to the core worlds which have comm relays anyway*, so the instant rewards from bounties and scan/survey missions feels mostly like a measure to prevent player confusion.
*well, unless the player builds a colony in a location without a comm relay and starts adding industries
If we're arguing realism, there would be three possible states for rep loss from combat:
- System has working comm relay: rep loss no matter what you do, since the enemy fleet transmits distress signals and other information about the battle
- System has no comm relay, some enemies escape: rep loss due to survivors reporting back
- System has no comm relay, no enemies escape: reduced or no rep loss
- Nonzero rep loss could result from rumors leaking from your crew
- And if we want to overengineer this, the chance of such leaks is based on your fleet size/crew count