Thanks , I couldn't ask for more, whatever your conclusion about it turns out to be. )
*Disclaimer, I'm not an expert on scanlines or the technicality thereof.
Anyhow, I kinda feel that if people knew what great looking scanlines actually looked like, they would probably want to have them on. But as I said the implementation of scanlines can be quite lackluster and downright ugly sometimes. Most people will turn it off and prefer the plain look without scanlines if this is the case, understandably. Some NES emulators has a basic implementation that is hard to make look better overall without considerable trade offs.
Another issue with a basic implementation of scanlines is that they only really seem to function properly when using integer scaling. If people turn on exclusive fullscreen without integer scaling on - something which doesn't seem supported by all NES emulators currently - maybe because they scale internally to the desktop resolution, I suppose, though that in itself shouldn't be a hindering - then it will look like a mess. That is, the scanlines wont match the pixels and it will look very strange.
Now, these issues can all be mitigated with a more sophisticated/flexible implementation. To me this seems to be what shader based scanlines can achieve, especially if HLSL based. MAME with HLSL effects is a good example of what is achievable. You can compensate for the scanlines causing a darker picture with effects such as bloom, and somehow even non-integer scanlines can still look good. Some smart tricks most be used here. Integer will still be preferable always, but sometimes you will lose too much of the screen to make it worth it, in my opinion. Also, If I understand correctly then one of the reasons that some scanlines will look better is because they consider the colors of the pixels and adjust appropriately, I could be mistaken, though.
Below is an example of two pictures, one which is a plain, the other with scanlines. I think these are HLSL shader based, produced by another NES emulator, should be easy to find out which, if needed. I don't know what the rivalry and/or work-relation is between different developers, I hope not to cause any offense. I'll even allow you modify my post with no hard feelings attached, if I do. But still, many emulators has the same kind of features, so I don't know what should be wrong about it. This implementation is quite good and works well in non-integer scaling as seen. Note that the image also doesn't become too dark.
Try Nestopia (remove the name if you prefer) in fullscreen with non-integer scaling (max) for a worse case situation.
Yes, I heard that this option can cause some glitches, and some games might even have relied on it in some ways. But I can't personally think of any specific examples, though. I might have been lucky so far when using it. But when it works properly, I think it's very nice option to have. It's of course a preference, and I can see the appeal of playing in the authentic way, also. The option could come with a warning attached, I suppose. Though, some concrete example should be behind such a warning, which it seems you have. Ultimately, I can understand if you do not change your mind on it for Jnes.
Thanks for reading. I'm not sure how helpful it was, but hopefully a little bit. )