You are mistaken. The climate control on Santa Fe is totally independent of the radio/navi system. It will not be affected. Also be sure you get a custom kit unit for Santa Fe (proper face plate, and PnP connectors including steering wheel). Don't buy a "standard" 2 DIN unit it will not fit. For a discussion about some of these Android units check this thread: http://forum.xda-developers.com/showthread.php?t=2110546&page=110 The thread is mostly about one type of unit (OUKU) but at least another two different models (S150) are discussed later. Remember, every unit type is different do not try to apply any hacks discussed there if you are not sure your unit runs exactly the same software (same unit model).
Many units can be found both as standard 2 DIN and also as a custom kit for different car types (different face plate but same software).