Unless the pick guard is glued to bare wood - a practice mostly eliminated - the pick guard won't hurt the top itself.
Some types of finish - most notably nitrocellulose lacquer - can be damaged by prolonged contact with certain types of rubber or plastics. The makers of electrostatic pick guards don't want to be liable for that damage, hence they warn that their pickguards should be removed after each use.
The answer to your question is that it depends upon the type of finish used on your Yamaha. If nitrocellulose lacquer, it shouldn't be left on the instrument for extended periods of time.
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