You seem to have multiple different questions.
To answer the one in your title, traffic shaping basically kills the benefit of squid caching, as it likes to shape the cache hits, which is exactly NOT the desired behavior (at my site, anyway) for items in cache. I've tried shaping and had that happen, so I turned it back off. :-
I've tried a byzantine and poorly documented procedure to try and make cache hits appear to be ACK packets and then give the incoming ACK queue loads of bandwidth (on the assumption that most actual ACK packets are going the other way, so you can get away with that) which sounds nice in theory, but in practice either from being byzantine, or poorly documented, or "darned if I know" it simply blew up and killed all traffic until I rolled the configuration back to a previous save point (be sure to make one before messing with the shaper - you may need it.)
It seems like a common enough combination (we cache to improve performance, we also want to Shape/QoS to improve performance) that there ought to be a more functional way to get there - but I haven't found it yet.
