Is it a bad thing? Only in the sense that if your computer suddenly dies in the middle, the software may now be in a spot where it cannot pick up where it left off. Essentially, your copy of MATLAB could now be currupted. This is the case in any such update, for any software. You don't want the battery to cut out midway.
So is it a problem if the computer is charging while doing the update? No. That would be a good thing, as it would insure your computer does not die in the process.
