Your first problem is not a problem,
Squid is a advance and well developed caching proxy servers, so it takes care that it always delivers the right contents , in order to do so it is not simple that when a page is viewed first time will be retrived from cache on second time. Few page uses no_cache directive which means it will never be cached by a good cache proxy server.
Now what is TCP_MISS, it simply means that the specified URL is not retrived from cache, TCP_HIT means it has been retrived from cache, whenever u find HIT then it is from cache,
BTW if you want loose caching then can look for wwwoffle
and also I want this IP address 129.41.xx.xx port :42xxx itz a online software, this ip&port should not go through squid [it should bypass].
what code to be put in iptables to make changes.
Are you asking to block that ip or port or want squid to not to do anything with it ?