The removal of a portlet war will not lead to auto-removal of its application registries and instances in pages. The registered application is still visible and available to be added to a page; however, it does not work anymore and the page will display a message like "This portlet encountered an error and could not be displayed".
So you should find and remove all the instances of the portlet from every page.
Redeploying a portlet
Both Tomcat and JBoss support hot redeployment, so you can just replace the old war with the new one and it should work. However, depending on the technology the portlet uses, the hot redeployment might not work properly. In this case, a server restart is required.