More to the point, it depends
how something is locked closed.
I can open the breech on a rifle (fairly) easily. The pressure released by a cartridge full of propellant, which exerts a force many times my strength, cannot - because it cannot interact with the locking mechanism in a sufficiently complex manner.
I'm not saying that a simple draw-bolt is all that's going to be on the outside of the hull of a starship, but the hatch isn't necessarily impossible to force with a reasonably easy-to-obtain degree of mechanical assistance.
Throw in a 'taking your time' +DM and a task chain to insert some sort of forcing mechanism (handheld ram-and-wedge or similar) and the roll can get easier. Still not if you're in a vacc suit, obviously.
So what if they used an emp device to shut down the ship and before it can reactivate used an outside system access to dump in an override say causing it to recongise a factory setting for example something like a simple password such as "0000" or "1234" as a viable means of entering the ship without setting off alarms because it would then register as an official part of the crew?
The problem with that is that if you've used an EMP to lobotomize the ship's computer, then you've essentially just stolen 100+ dTons of inert metal.
Getting malware onto the ship's computer is a fair idea. It works now, and there's no reason it shouldn't work in the future, since Agents will increase in complexity with TL to match the victim. The trick is getting it onto the computer in the first place, which generally will require some sort of 'human' element (like a guy in the port authority who can piggyback it onto the navigational downloads).
Frankly, a psion is cheating, but it is a very effective option. No ship can be expected to be secure against someone with teleport, microkinesis, or similar abilities.
And, ultimately, nothing is ever designed for perfect security. As stated repeatedly, you can create more-or-less perfect security today, but people don't, especially for 'civillian' vehicles. Engines and power supplies are accessible via maintenance panels (the bonnet). 'Keys' are a signal that's only as complex as it needs to be - hence why you can sometimes find that your keyfob opens the car parked next to you. Yes, at TL12 you could fit smart-encrypted biometric everything. But unless human character changes drastically, I can assure you that most people won't, because, as said, it's 'too much trouble'.
And as a result, someone will be sitting in the next hangar with a computer, and will snag the key-code out of the ether.