Right now, you can only get hit with a toll once every 30 days within any given system. I'll probably change it so that it's once a month per system per faction, though - otherwise, it's exploitable, as you could get stopped on purpose by a faction that doesn't consider your cargo illegal and then have free reign for a month.
A time base system can be played, how about just a simple 'flag' that lasts until you dock. Not like you will specifically target freighters with illegal goods after you get scanned to sell back without the danger of getting inspected again. That just seems a very round-about and hard way to make credits when you could be doing almost anything else.
As for the frequency itself, to be fair i'd consider it differently while still tied, as a separate event, to reputation. Say you have a base standard 50% chance of getting searched per faction initially. If you get searched and are found with contraband, it gets bumped up to 60% chance, with that faction, and say it scales down universally with other factions (55% say), up to whatever limit you see reasonable, 90%/100%. If you often smuggle and get caught smuggling, you'll be targeted more often, and eventually raise that chance even with factions you don't trade with.. 'being notorious'. This will fit in with the reputation system that if you do get caught and they look the other way, it won't affect that chance more.
If you engage in legal trade, get inspected, and found all clear, that percentage drops. If you carry food to starving children and medicine to far-flung worlds, i'm sure everyone eventually will think of you as a trader-saint, even if you do eventually end up smuggling some drugs with the medicine. Still, this should be capped at say 10% just to make sure you can't 'saint' yourself in consequence-free smuggling.
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Aside from that, any way there could be a situation where i'd suck in the fines and STILL make a profit off smuggling? That'd be broken. I don't think you mentioned if the inspectors confiscate your contraband or not? If you can't pay the tolls they should just rob you blind.
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Oh, and as a last thing, would it be possible to target periods of high activity, when inspectors are overrun with scanning other fleets (if that even happens), so you can make a break for it? I'd love a lot more interaction and gameplay on the galaxy map.