That could work if your opponents comm & computer system was designed and implemented by your military. Otherwise, designers are not that stupid without 1st having a lobotomy.
I'd agree shutting things down remotely seems unlikely.
The comms channel simply isn't going to be tied into things like life support or engines on a ship not designed for remote operation*, and if there's any security software installed, that's where it'll be. Hacking into a ship and killing it over a comms channel doesn't seem realistic. Working by the rules, you'd essentially need an
Agent programme on the ship's computer network to do anything, and these require a 'non-trivial amount of bandwidth to transfer', not to mention that simply yelling binary at someone does not force them to accept the call or to run the software even if they receive the message. If you can get your TL14 Agent software onto the ship somehow before the event** and time it to trigger at the right moment, though, go right ahead.
If you're actually part of a boarding party on board, then it becomes something more realistically achievable.
Yes; you can have an essentially unassailable secure network but most computer systems on most starships are civilian models - the primary requirements on the designers will be the same as electronic devices today: ease of use for the non-computer specialist, ease of interface with other commercial-off-the-shelf-items and software, ease of maintenance/repair, use of standard parts and low cost.
Which is why - for all that computer power and encryption may improve by orders of magnitude - human stupidiy is still likely to allow someone who knows what they're doing to put one over on someone who doesn't.
Equally, lot of designed weak points will probably verge into "electronics" as much as "computers"
A civilian ship, for example, whilst fitted with 'security' is likely to be designed above all else to compensate for idiots; such that it is absolutely impossible to accidently kill someone by venting the compartment they are in, opening the airlock doors in the wrong order, trapping someone in a deck that's on fire, etc. This is going to be controlled by hard-wired stuff (possibly even mechanical interlocks) which the ship's own software is designed not to override. Which means, if you can get physically on board and prat around with said interlocks with a multitool, you might well be able to pop a release on an iris (for example) despite the software saying "stay locked".
Note that this wouldn't work on a military ship, or a paramilitary ship (corp mercs, police, etc), or something explicitely designed to be carrying valuable cargo (like the 'treasure ship' freighters seen in Pirates of Drinax) because "active sabotage" is the sort of thing that pops up in requirements specs. But for civilian hardware it's always going to play second fiddle to safety and ease of use.
* By comparison, with suitable software and skills, 'jacking' a civilian probe or drone seems reasonable because they
are.
** Top of my head, most ships use commercially bought-in jump astrogation data. Hiding something in the jump download might be doable, and that by definition has to be connected to the ship's engines/navigation systems.