Penalties waived after expiration of 90 days visa

Does anybody knows If Honduras will waive the penalties if your 90 days visa has expired

I think I saw something about extensions and fee reduction online somewhere, but now I can't find it.

You can try calling the Honduras Immigration hotline at 2232-7800 and see if they can help you more directly.

Have you heard anything lately about  about penalties due to covid19

The immigration offices are open for the last few months and I would doubt they would do another extension they did last year.  Penalties are posted in the office now and its not cheap.  Even for one day.