Does Mac App Store accept application written in Python/Java/Ruby?

Yes and no. Apple doesn't care what language your App is written in, but it cannot depend on or install anything outside of the binary you submit to Apple. The relevant guidelines are below:

2.14
Apps must be packaged and submitted using Apple's packaging technologies included in Xcode - no third party installers allowed
2.15
Apps must be self-contained, single application installation bundles, and cannot install code or resources in shared locations
2.16
Apps that download or install additional code or resources to add functionality or change their primary purpose will be rejected

So, while this means you can't depend on Ruby or Python, you could use a framework like MacRuby to build your app in Ruby and embed the Ruby interpreter. Speaking for MacRuby, apps have been successfully submitted to the Mac App Store this way.

AFAIK, Cocoa will allow you include code written in different languages (including Ruby and Python, but not Java I don't think).

Check the Apple SDK's for more info, but I believe (thanks to Cocoa) it's not a problem.