I'll post for my own indie, as I try to use him as a model for how I believe a pirate should operate.
1) Traders mostly. I've pirated the occasional "other" ship when there are several people on though.
2) I pirate nothing below level 45, doesn't matter what it is. I try to RP with people in lower class vessels than the Transport, but I don't usually pirate them for anything.
3) I do not tax empty traders.
3a) I do indeed if they ask for it, however I'll usually leave them alone after they've paid me once.
4) I go by percentages of their profits, roughly. This allows me to make it fair for everyone. I usually go 20% of what they will be making on this leg of the run give or take a bit.
I know I'm not bankrupting them but I'm still making a nice bit of profit myself.