According to this quote from his voice actor Thomas Spindler that I found on the Wario Forums (your #1 place for Wario discussion):
“This is 100% correct. Wario speaks German: he says (or rather, I say) ‘So ein Mist!’ The recording was done in a studio of the former Nintendo head office in Kyoto (not the new Nintendo premises in Kamitobaguchi), under the direction of Mr. Takashi Tezuka. Back then, I worked on the script for another Nintendo project with my French friend and colleague Julien Bardakoff (who voiced Toad/Kinopio). My company T.S. Word Co.Ltd. also translated and edited the German script for Star Fox which can be verified in the credits of Star Fox 64. The concept behind Wario was that of a German character and those responsible for the voice-overs at Nintendo back then intended him to speak German. I hope that this resolves the issue once and for all.”