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I have some .java files that I want to view/edit in Notepad++, but I am not sure how this will affect other programs. Would the compiler still be able to compile them, or would I find some issues?

I would check .java files, but I would like to change some other types to be opened with Notepad++. And I dont want to go back and change every type back to "default" program.

Can I set one rule for double click and another rule for command line for example?

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Changing the default program to open a file extension won't affect the behaviour of other programs that use that file, so opening your .java files in Notepad++ won't be a problem when compiling them.

If in command line, you can use the program name if you want to open with a different program than the default, for example:

notepad.exe test.html

As long as notepad.exe is a recognized PATH, of course.

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