Plenty of scripts will give "deprecated" messages with Gimp 2.9, because it's a "development" release. This doesn't make them buggy. If you make a private copy, it will "hide" the official copy and you may miss other more important fixes. I think you can squelch these messages with the proper parameter in your Gimp shortcut:
In 2.9.5 you are likely to have "warn" by default, and you would just have to change this to "on".
Code:
--pdb-compat-mode {off|on|warn}
If the PDB should provide aliases for deprecated functions.In 2.9.5 you are likely to have "warn" by default, and you would just have to change this to "on".