Is it ok to build a Niche Site using my subdomain? for example: http://nichestore.mysite.com Will it still be profitable?
you can do it if you want. will it be profitable? Just as profitable as it would on a non sub domain.
Google used to treat subdomains as separate domains, but apparently they don't do this anymore. Subdomains are treated like directories: e.g * nichestore.domain.com * domain.com/nichstore are treated the same. Buying a separate domain would of course be better. But I use subdomains for different niches, and it's working for me
how about domain mapping? buy a new domain and mapp it to your existing website or store's subdomain .. no need to install the script again
Yes, no problem you have one or more sub domains, you have to work on it as a new domain, as a new site. you need to be careful during optimization of sub domain.