You custom application pages are accessible across all the web applications and can be access using the \Layouts folder, so doesn't matter if your WSP is deployed globally or to a specific web application, your custom pages will be accessible from all web applications.
As for deploying Visual Studio 2010 WSP to a specific Web application - SharePoint will only deploy to a web application (or allontenturls) if it needs to to modify a web.config file, like for instance if it is inserting a safe control entry (in case, if you Visual studio solution contains Web part or user controls). Or solutions dll needs to be deployed to the BIN directory instead of the GAC etc.
Follow this MSDN blog for more details.