In case of usage ExtendedLengh the APDU buffer size is 32 KB.It is up to 32KB. In reality it is around 8KB from my experience. This buffer is limited by the amount of RAM on the card. It would not be a good idea to have the APDU buffer in EEPROM since it is accessed often and needs to be cleared at the end of a command. This would be bad for performance and would end up wearing out your EEPROM.
If your card has a 72KB EEPROM therefore you should have ~ 72-32=40KB card memory for your applets.