I actually like then setup I currently have (Lilypond + Notepad++ with custom Lilypond language definition for auto complete and syntax highlighting [the definitions file is out there on the Internet] plus Sumatra PDF as a viewer that allows PDF updating even when open - one custom Notepad shortcut for compiling with NppExec and that's it). The only part that is hacky is the referred "textedit" links because somehow internally, when lilypond generates them, it assumes that one tab equals 8 spaces and this is actually editor and configuration dependant (so it seems there should be a way to set tab size for textedit link calculations within Lilypond, which I do not know if it is the case).
In consequence, I have some nasty calculations in a custom script for textedit:// links to actually land in the right column in Notepad++.