I just tried one of the battles (The Emerald Nebula, Normal difficulty) for the fourth time or so, since I was testing anti-armour, unshielded Rebel designs. The deployment screen clearly said I would get over 2000 honour points if I won the battle. I did, but got 0 points, for some reason.
What’s the problem? I’m using version 1.24.
Do you get honor for a given difficulty level if you have already beaten it?
I can’t remember, really. I won a previous battle and got honour, but I think I lost others before winning again and getting 0 points.
I thought I heard some people ‘farming’ missions for honour, so this struck me as a bug. Might be wrong, though.
PS: Perhaps you need to beat your score in the same difficulty level to earn honour again. Who knows.
Ah, I think I’ve figured it out. You get the difference of honour between the highest achieved and the current victory’s, in a given difficulty level.
So if the ‘high score’ of a particular mission is 2000 and the current battle’s deployment phase states you’d earn 3000 if you won, in the end you’d get 1000.
This is true, and done specifically to make it impossible to ‘farm’ honor 
A wise move. 
It might be better if the deployment screen showed the previously achieved honor on it (perhaps as a tool tip on the existing box), and if the victory screen showed the subtraction taking place when it tells you about the honor you earned.
yet after finishing 4 missions on all difficulties and i have over 20k honor left and all modules, ships and races bought.
GCB need more stuff! not enough! MORE !
EDIT: played a couple more maps … got 100k honour … 
where should i put it in? .)
I’d pay large quantities of honor for gold plated bling spikes on my beloved alliance ships.
I wanna blow things up in style.