Whenever someone programs something into the computer, they call it a subroutine. I’ve only ever heard this in the context of assembly language, although it seems hard to imagine that it could be so common to just whip up a complicated subroutine in assembly while under pressure.

That being said, I’m sure every byte counts on a starship, so you’d need something that lets you manage memory safely. Just speaking commands into the computer wouldnt cut it. For small probes and such they’d probably use something like Forth, similar to how it’s used today in industrial and astronomical machinery.