Pirates are probably one of the easiest things to counter... as Castus said, all those cutters in a normal fleet do jack all for stopping the pirates from occurring. place 5-6(5 minimum) cutters in your defense tab with a basic level 1 naval station in the system and you'll likely never see a pirate there again, unless a pirate base(new with EoF) happens to be somewhere close by, but even then it won't be every turn, and you can take out the base to stop that. Have systems in a province also reduces piracy chance as well(and increases profits between provincial trade!). There are some players who actively encourage piracy so they can "farm" the pirates(it's like 50k or so per pirate ship killed), or continually attack the pirate base if they find one, but just kill the ships each time and leave the base.
As for percentages, a Naval station does not reduce piracy rate by 2%.. if you don't have a naval station piracy rate is actually increased by 2%, so having a naval doesn't affect the base chance, just removes the additional percentages. Also pretty sure those percentages work like the random events % chance. Basically that percentage keeps going up each turn, so that 2% goes to 4, then 6, then 8 and so forth until a pirate encounter happens, then it resets to it's base value and starts counting up again. trading with systems not in a province I imagine also increases the % chance as well, however the 5 cutters+ naval per system will get rid of most of that.
Building cutters is no more or less micro then building those civ stations you need to have to be able to even trade. Simple suggestion, you get access to cutters as soon as you get access to civ stations. while your system is getting ready to build and upgrade the modules for it's civ station, it's not currently trading(there won't exactly be any freighters yet either), so why not just build your cutters at that time, you know you're going to need them(even 3 active cutters with no naval is better then nothing). First system you go into build mode for, just que up 5 cutters then save them as a favorite invoice, then just use that favorite invoice for all your other planned trade systems to save some clicks if it bothers you that much. Cutters are quick to build compared to a normal cruiser, so it doesn't take long even for a really poor IO system to build them relatively quickly.
There's also the convoy system tech you can research(right above commerce raiding in C3) which gives a big reduction to piracy chances(60% off) for whatever system it's turned on for, at the cost of a 5% loss in trade for that system, and even if there is an attack, all the freighters will spawn together, near your planet and with any cutters as well, so much easier to defend. That tech is also the solution for Loa trade(especially if combined with q-ships).
Also, the randomness and isolation of your freighters by the pirates when they do occur is supposed to be frustrating and a good chance you'll lose a freighter.. otherwise, why exactly would the pirate risk his neck? They've been hiding(there essentially all stealth armor equipped ships with low signature weapons), lying in wait, in or near your system, for just that opportunity to hit your vulnerable freighters and make off with the loot.
