Since scripts frequently refer to layouts in one way or another, I think you'd want to keep them in the same file as your layouts. You can put all layouts and scripts in one file and your data tables in another. This is a known technique for separating your data from the interface.
With this approach you can:
Put a copy of the interface file on each client machine and host the data file on your server. (This is supposed to reduce the amount of data that needs to be pulled from server to the client and thus improve performance for shared DBs. I haven't tested this, so I don't know how much it helps with current network technology and the latest install of FM Server.)
Distribute an upgraded interface file to users without having to import data from existing files unless you've changed the table design.
You now have to maintain two files instead of one and need matching access privilege settings on both.
There may be other pros/cons but that's what comes immediately to mind.