Most Pirates aren't trying to take the ship or the cargo but the people for ransom money. So I don't see them having any qualms about fucking a ship up.
They can ask for more money with unharmed cargo, and it gives them something to destroy if negotiations are negative before they have to start killing hostages. Doesn't mean that all pirates are smart enough to think that way, but there's plenty of good reasons to care about the safety of ship cargo and crew together and not just any one of the three.
I haven't had to deal with east Africa pirates but had a helicopter being shipped in a container to Cameroon that was hijacked two years ago. They ended up only spending a short time on the ship abducting the captain and one other Sr crew member before fleeing. Initially we had word that it was hijacked and the entire ship was being ransomed but in the end it was much easier and effective to just ransomed a couple of key crewmen. Took an extra week or so to get back on schedule to deliver the container with our helicopter in it. While some would keep the cargo and have the means to distribute it to the black market, that is a huge undertaking and even holding the ship will cause escalations rapidly. While a shipping company might negotiate for the release of the ship and cargo, some of the entities that are shipping may have other means of getting their possessions back. I can promise that if it was the US embassy in Cameroon who had new armored SUVs on the ship there would be a different response to the cargo being held than a nonprofit's helicopter. You don't last a long time if you take risks like ransoming an entire ship and cargo when you don't know who's cargo it is. Also while possible to jam all the GPS trackers, there are so many individual ones attached to containers that it is hardly practical to get a ship off the map. We were able to watch the entire thing in real-time while waiting on word from the ship line as to what was happening.
Fair enough, I'm not planning on going pirate any farther than maybe the next pirate fest in Portland, personally if my payout from whatever crime was to be committed is less than 10m it's not worth the potential risk. Even then it'd have to be a pretty sure thing for me to consider, and of course I wouldn't be willing to participate if there was significant risk of anyone getting hurt. Even going up against an 'evil' corporation all the people protecting the place are just employees doing a job, very few of them are probably financially stable enough to make a moral judgement about where they're working, assuming they're even aware of the 'evil' the company is responsible for. (Evil in parenthesis because it's entirely hypothetical)
There are a lot of ships at sea and they have radars and this is one way to locate missing ships, they see quite far and if you're trying to evade detection you also ought to turn your radar off because it will be the first thing they'll spot. Even then I don't know if ships are exactly equipped with radar warning systems to facilitate radar evasion! And the other thing is that for being able to process the stolen cargo you will need a big organization in place, organic or inorganic. Either way, if it's big there are more risks of infiltration and double crossing. Also, it tends to take time to build an organization with those capabilities, thought not always but tends to. And taking time to build up that level of operation and combining it with the potential risk that one of the containers or the ship itself is of interest to American or Russian military - you're inviting an army of angels to descend upon you. It's like the equation of "shall I hit the main vault of a big central bank for 1 trillion in gold bars or a side office and get 1M in cash" - sometimes the loot is such that you cannot even liquidate as much of it into cash as you could from a simpler gig. And the heat is going to be enormous, wrath of God level. Whereas the easier target is an easier target, the whole thing is over quickly, your life is still transformed entirely and not even a fraction of the level of heat.
