I haven't had any problems at all with combat readiness unless I do something foolish like waste a lot of CR pursue'ing ships I can't possibly catch.
If you're attacking enemies, destroying ships, salvaging, and leaving to look for another target... it's hard to find that another target before most of your CR is back? sure it varies, a 30CR deploy ship might be useful twice as often as a 70CR deploy ship?
I think the main flaw is purely economical... being able to hunt poorly defended buffalo for the massive bounty in supplies each one carries. if supplies can't cost less, maybe ships should cost more? if ships can't cost more...then the problem is purely of enemy fleet layout... large freighters with tons of supply inside them shouldn't be defended by a hound and a talon fighter wing.
most buffalo pirate fleets as they are now might make sense if they used hounds as their freighters, or if freighters and freighter rewards were totally rebalanced.... basically hunting enemy freighters is just too important now that 90% of your income comes from selling freighter supplies... this means killing enemy combat ships has almost no reward unless those combat ships are escorting a freighter... advancement in starfarer .61a campaign mode is basically just about how many freighters you can kill. yes this is a problem. however I do not think this problem is because of CR and supply, it's just another problem that CR and supply have highlighted.