The only difference between .wav and .aiff is the 'endianess' of the header file both are PCM wave files.

FLAC files are asymetricly encoded so all the processing goes in to the encoding (which is why there's a 'quality' setting when you encode, it doesn't affect the quality of the sound (they're all lossless) but it affects the resulting final file size - smaller file more processing to encode).

The processing power required to decode a FLAC is negligible and shouldn't cause even the slightest strain on any computer released after about 2005.