Yes. It can affect an empire quite drastically..
I know of a case where the exploit wasn't noticed by the enemies, nor the host. It went on for 30-40 odd years.
The player using it didn't know it was a bug and didn't even realise it was happening.
He didn't even use it for every fleet, but it was used for sweeping or scouting iirc. Don't know the exact details.

Imagine the condition of the host here.
Is he supposed to dole out a tough punishment or a lenient one?

In my own gaming experience, I was playing a test IS One World Race that was meant to kill 1 neighbour and die fighting a 2nd neighbour..
Sadly, a mine dodge penalty cut out my intel gathering AND part of my fleet...
3-4 years later, my OWW station died against a jihad DD fleet and obviously died soon after.

ps (what the hell was the shortform for that.. OWRace/OWWonder?)

either deciding the punishment before hand (slightly tough, as it depends on how much it's been abused or taken advantage of).. or allow it all together... (which I don't really like as it removes the few advantages of minefields even more)...
I guess the host sending out an email explaining the bug (so that enemies can spot it too) + a standard punishment?

There seems to be no way to standardize the punishment, that means that we come back to the same point.. the effects can range from one extreme of crippling an empire or allowing it to get away with a substantial advantage.