For the monthly profit, I'd suggest the weighted average of the possible profits.
Regarding crackdowns, regardless of realism, I think it would be better for gameplay if they were something people wanted to avoid. I just think the decisions about how to avoid being found and how to defend are good parts of the game; but that only works if base assaults are something players want to avoid.
If a player sees an crackdown sentry and fighter, they should think "I'd better shoot that down before it finds the base"; and the player should have built interceptors for this purpose. If the enemy is flying heavy gunships or something, hopefully the player should have their own heavy craft to defend. If the crackdown arrives, the player should hope there base defences are enough to help them... But on the other hand, if the player actually wants there base to be attacked, then all of the planning and preparing and fighting becomes "Cool. Crackdown. I'll just do nothing and wait for them to arrive." I just think it's more interesting to act than to wait. (I personally 'role play' that I need to protect my bases from being attacked regardless of the profits.)
I've not sure what (if any) changes would be good for crackdowns; but I do have one suggestion:
Damaged tiles in your base should cost money to repair. I'm not talking about whole facilities being destroyed, I just mean there should be costs to repair the base after various explosives have trashed the place. That way, if you win a base defence you'll still be awarded with good equipment and high ranking prisoners, but you'll have to pay a price too... Maybe you'll have to sell the equipment you got to repair your base. The cost could be based on the number of damaged squares on the battlescape at the end of the mission; and it could be deducted directly from your account.
Anyway, that would probably take a decent amount of work to implement and balance; so maybe it's not worth it. But I thought it was at least worth suggesting.