When an app is closed with the Home button, it is frozen in RAM, not completely closed. This is usually an advantage, since it lets the app open quickly to it's last run state, allowing for quick switching between apps.
In your case, however, the app starting where it left off means it starts with the last file open and already unlocked.
I don't know of anyway to change this behavior in Numbers. I know it is possible, because I have apps that require unlocking every time they open, so it's most likely an oversight on Apple's part. Although it won't have any immediate affect, I recommend leaving some
feedback with Apple. They are probably already aware of the issue, but the more feedback they receive the higher priority the issue should get.
In the mean time it should not be necessary to restart to reset the locked state of the file, though it will require a few more steps.
One option is to close the file before exiting Numbers. I haven't experimented, but unless you've turned on the Remember Password in the file's preferences it should require the password every time you open it from the file list. If it does not, then add that to your feedback.
The other options is to clear the app from RAM. To do this double press the Home button to get the multitask bar, find the Numbers app, then swipe up on the thumbnail above the icon. This will remove the app from RAM and force a clean restart the next time it is opened
Restarting the iPad does this for all apps; though it does not remove their icons from the multitask bar.
Good luck.