All files need encoding. WAV is a form of encoding. The audio on the CD is encoded in a certain way. Phonograph records are encoded in a certain manner. Even the signals going over the wires to your speakers must be encoded in a certain way. And, as I'm not sure that you're completely following, FLAC introduces zero artifacts (barring bugs). It's like ZIP, except optimized for music. You get back out exactly what you put in, bit for bit.

What I'm wondering is why you're so interested in WAV files. I understand that it would take a while to compress them (which could potentially be obviated by encoding them directly to FLAC when ripping), but if you're not listening to them directly, why are you interested in having them? If your reason is that you might need to reencode them into mp3s (or WMAs or whatever), FLAC decompression still works much faster than mp3 compression, so if you just pipe the output of flac to the input of lame, since flac is presenting data faster than lame can accept it, you're not losing any time, other than, possibly, a few milliseconds per song for it to present its initial data. That is, the bottleneck would be lame, not flac.