In HS, there is a default NPC tax on top of player taxes.
There is no bulk discount for taxes. Try looking around for poco’s with lower tax rates, train custom code expertise to reduce NPC taxes, design setups that minimize how much taxes eat into your profits, or do PI outside of HS so that you no longer have to pay the NPC tax.
I’d imagine that taxes are based off of the estimated item value (which is the estimate you see when looking at items in your hangar or cargo, in the fitting window, and so on. How that number is calculated is apparently a bit of a mystery. See Fuzzy Steve’s post if you want to know more.