If you're gzipping/deflating your HTTP connections, 100 304 response headers are not going to be your bandwidth bottleneck. Even if you are not, a 304 response has at most like 200 characters in it, 200 x 100, 20 kilobytes in headers responses, not exactly earth shattering.
Since you brought up the caching issue, when you change any resource in the bundle, you are going to have to redownload the whole bundle. The bigger the bundle the more likely that one of the resources inside might need to be updated over time. With pipelining you only have to retransmit modified resources. This is not even considering the higher likelihood that larger objects have of getting thrown out of the cache.
Also, most of the overhead in establishing a connection over a non-negligible latency internet connection is in the TCP handshake. Not in the time spent transmitting a few packets of headers.