They don't combine particularly well. In fact, they have a nice anti-synergy going.
Let's take an example. Assume you have a trade route with 100 max piracy that you're finally deciding to do something about. So you build a citadel with 90 trade protection, which cuts actual losses to piracy down to 10. So far so good- but you want to get rid of the last 10 points as well, so you send in a few corvettes. Nothing happens. You bump the fleet up to 10 corvettes just hanging in the same system, but still nothing happens- your corvettes are not doing anything! That's because 10 corvettes giving 100 piracy suppression still won't cause the piracy levels to budge- even if the actual piracy losses are just 10 due to trade protection from the citadel. So you bump the corvette fleet with a few more ships, which finally gets rid of all piracy after a while- at which point you realize it's now your citadel not doing anything.
It's a pointlessly complex nuisance. The smart solution would be to just merge the two concepts into one, so fleets would provide protection and stations suppression.
This is what I originally thought was the case in my OP before I edited it. It is not quite right though. When you mouse over your system you get these numbers (Using your example):
Trade Route Value: 100+
Max Piracy: 100
Piracy Effect (PE): 10
Current Piracy (CP): 100
Trade Protection (TP): 90
The PE is what actually cuases losses to trade value. In this situation PE: 10 means you lose 10 trade value. If you move in a fleet of 10 corvettes, which each give 10 suppression each, that would be 100 suppression so it would gradually drop the CP down to 0. The thing is, that doesnt happen instantly, it takes a little while. if you watch the number will go down, but you might need more than 10 corvettes for the CP to go down to 0 in the time that the patrol spends in system. But stationing 10 corvettes would eventually reduce CP to 0. Having 10 corvettes pass through might not be enough though. Sending 20 would double the speed at which CP drops, which might be enough to bring it to 0 in the time it takes your fleet to pass through. Then depending on how long it takes your corvettes to come back on their patrol, the number will grow again.
This is where TP matters, while you might not be able to get CP at 0 with a 10 corvette patrol. You should have no problems keeping it under 90, which means the trade is safe. PE is equal to CP minus TP. If TP is higher than CP, then CP does not have any effect other than giving a chance of spawning a pirate fleet.
Keeping CP at 0 prevents fleets from spawning. Keeping PE at 0 prevents losses to trade.
In the above situtation, parking 1 corvette in the system would be enough to lower PE to 0 and protect your trade, because it would permanently drop current piracy to 90, which would be countered by the TP value. But you would need to park 10 corvettes to bring CP to 0 and completely prevent any chance of a pirate fleet spawning.
