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Perhaps not the first time the question is asked, but I could not find anything similar. When a file is deleted from a project, it is physically deleted from the disk. Most of the time this is not what I wanted.
There is no delete from project action. Delete is always physical. This feature is heavily dependent on project type. There is no generic project format. In J2se project you can go to Sources panel in project properties and configure Includes/Excludes. Then the java file disappears from projects view. (So in a way it's implemented already) In maven projects it's likely not possible to hide the file but you can exclude it from compilation by configuring the maven compiler plugin.. etc..
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss