In certain cases (eg Geodatabase), IxxxProxy classes are always needed as an alternative for casting; casting and instanceof do not work for these classes. We don’t have an automated way of identifying which cases those are. So, if the IxxxProxy classes are deprecated, user’s code will show deprecation warnings, and they will have no workaround to avoid some of those deprecation warnings.
Also, by deprecating the proxies, all existing code will need modification to get rid of lots of warnings caused due to the programming pattern followed at 9.0 and 9.1.