During the transcoding process, does foobar2K decodes files always firstly to WAV? For example, is the effect of converting APE files to MPC files equal to endcoding orginal WAV files to MPC files using foobar2K's converting function?

Since wav is a container format no it doesn't decode to wav. But it does what you suggested, yes. It decodes to PCM data which is what you normally have in wav files:

wav --> mpc = wav --> ape --> mpc