How do pirates choose their targets? Well, they like rich planets of course
Trade ships, lots of built up installations, etc are all attractive to pirates. If there is an asteroid between this "rich" planet and the pirates, and there is a big bounty on you, chances are high the pirates will just jump through your asteroid to get to your rich planet.
Maybe the pirate targetting theory should be restated as "Nearest settlement to their base that is worth their effort (size of attacking pirate fleet)".
So, if the pirates are appearing in places where you did not think possible, you should double check if there is some back-door route somewhere where the pirates are using. Another more likely possibility is that the pirates are skipping one of your choke points becuase there is nothing there worth (for them) to fight for. So they fly through your chooke points and go target a big(er) planet with trade ships and stuff and earn more credits.. I've actually had to chase some pirates through my own space with my mobile defense fleet before 
Some solutions are if you are sure of the path the pirate takes from their base to whereever it is that they are attacking, then you should add phase jump inhibitors to your defences at those chokepoints. This makes it harder for them to get through to the deeper areas. And yes, putting some cap ships there to gain some exp is a good thing. Helps boost the choke point defense too.
Now, a point about upping the bounty and bidding. I just wanted to point out something about the pirate bidding that doesn't get mentioned much for newbies.. The length/strength/intensity of the pirate attack is directly porportional to the amount that was bidded. For example, if there are 1000 credits against you versus 250, the pirates will attack with a bigger force for longer. Now, consider if you enter a bidding war against the enemy, and the bounty sky rokects. And you lose the bidding war - oops... Conversely, note also, that what was bid against you (the bounty on your head) stays even if you win the bidding war. This means that when the next round of pirate attacks come by, you have to outbid even more! Personally, this is like throwing more money into a bad investment bank.. So, my personal feeling is that (esp. for newbies) unless you 1) need if for tactical reasons (distraction etc), or 2) are really in a bad spot, try not to bid on the pirates and take your licks like a man..
Cap ships need loving experience too..
Lately, I've had this feeling that the pirate fleet gets larger later in the game even if the bounty is low. Simply that the pirates will give up earlier ("There is no more bounty to be gained in attacking").. But this affects the pirate targetting theory above..
Anyone care to confirm?
EDIT: Sorry, just to be more clear, if there are more than one equally "rich" planet for the pirates within the same distance (jump), the pirates tend to alternate from one to the other..
Pirate targetting theory: "Nearest settlement to their base that is worth their effort (size of attacking pirate fleet), alternating between similar sized/worth settlements of equal distance"