Ape as a codec is very expensive in terms of CPU power, so your experience with the Fuze would have been better with flac.
It's possibly not the clearest wiki page to prove this point, but have a look at how quickly ape is decoded on here
http://www.rockbox.org/wiki/CodecPerformanceComparison#Current_Results and bear in mind that 100% means it decodes it *barely* fast enough to play in realtime.
Results on one player (Sansa e200 v1 series) show that ape gets around 60 - 95+% whereas flac is around 600%, i.e. an order of magnitude "cheaper" to decode. While I'm not sure about the architecture on the iPods, this is at least an indication that flac is (currently) better suited to Rockbox than ape is, and as both are lossless codecs I would convert ape to flac.
And for some anecdotal evidence, I've used flac files on an iPod video and Rockbox has coped with them perfectly.