In case anyone else stumbles upon this:

A workaround (?) for this problem is to manually set the "ulimit" to a number that works, e.g. open a shell run
and then start SH3D from this shell.

Now, I have absolutely no clue of java and have no idea if it does anything else, so use on your own risk.

That said, it seems to only affect the shell it is run in as in another shell, when I run
it still returns "1024", as was the case in the shell I tried running SH3D from when it did give the error from the post above.