True, but your CPU is limited too so having to lex & parse sourcefiles and walk syntax trees to run programs could be a bottleneck there, if you remember old computers there was a significant performance gap between native and interpreted code.

In practice that might not matter for many applications if they do not have to use intensive algorithms etc.

I would still imagine that compilers would be used more than interpreters though which would mean that some security would need to be present at the "hardware" or "firmware" level.

Another interesting thing to think about regards backing stores:

I assume that the programs will be able to take input from the world around them, i.e other ships , objects in space etc.

So what's to stop you from using (perhaps) a tractor beam to re-organise the position of asteroids in space and then "read" that data back using ship instrumentation?

Potentially the entire universe becomes one big DB!