"Flowers and applause" sounds most natural. "Applause" is most commonly used when referring to an entire audience clapping. You do not make applause plural.

Yes "Flowers and applause" seems right. "Flowers and claps" is just wrong as 'claps' does not mean 'applause'. You can use 'clapping' to mean 'applause' if you like but somehow it does not sound too good. By the way, your question should have been "Can anyone tell me which one should be chosen.........".