The polyurethane based sealant I use (Folk Art Artists' Varnish) is waterproof. I still wouldn't submerge a custom pony as water will get in from the hairline and probably cause the paint to flake. Perhaps a seapony without an FBR might be able to come through without damage, the varnish should be able to protect symbols and eyes.
For regular ponies it works amazingly, however. I've never had any problems with boil perms even though I never manage to keep the pony's body from getting wet in the process, no matter how careful I try to be. I still try to protect the pony by placing a towel or something between the body and the hair, just in case, but I've never noticed any damage on the sealant or paintjob.