I would say it probably messes up things. They are probably references in the other files.
I can't say for sure but you can always try..Backup your files to somewhere safe, then rename the copy and see how it works out
EDIT: Answer from the pros on twitter: No you can't
https://twitter.com/TheSimsResource/status/617640898898325504
If the reason you want to change the names is to know which file belongs to which house/sim/..., there's a not official tool for that: "Sims 4 Tray Importer". Once installed (it's only 3MB), it shows you the content of your Tray folder, with the information you would see in the game gallery and which files from Tray form the house/sim/...
It also lets you export your content to a zip file, containing the files from tray and optionally the mods you have used. If you are a creator and you share your content, you don't need to check which CC you have used for each creation anymore.
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