In Google Webmaster Tools under Search Traffic --> Internal Links, for some pages it's showing too many internal links. Is there any effect on my site due to these internal links. How these internal links works?
For Example:
Under /musical-instruments-2 it has "Top 82 links" and "Total links 470". I observed that it contains unrelated links (other than musical instruments). Why has it linked unrelated data under musical instruments?
The "internal links" are the pages that you link to on your site the most. It is saying that you have 470 pages that link to /musical-instruments-2.
When you click on /musical-instruments-2 it lists the pages that link to it. If there is anything in there that is unrelated, it is because you have an unrelated page that is linking there.
Most sites usually have some navigation on every page that links to a few top pages. As such, there are going to be links from many other pages most of which are only loosely related. This is so common that is is never a problem for Googlebot or search rankings.
/musical-instruments-2? And the pages listed in Google's report (when you click on that target) are not correct?