I've hears this a few times and it's weird. When I have long nails, I have a hard time getting the pen out. I don't use my nails to *pull* my pen out. I push it in and it ejects out. When I have nails, they are in the way and I can't push the pen in with my fingertip because my nails are in the way. I don't want to push my nails into the pen. This leaves me doing a weird maneuver where I use my knuckle to push the S-Pen in to get it to eject and then open my hand back up to grab my pen.
Now, all that being said, I love my S-Pen because when I have long nails it's really hard to be pin point accurate on the screen. Again, I can't use my fingertips, I have to use the pads of my fingers to select things and it's just not as accurate. So I use my S-pen almost all the time while using my phone.
For the record, I don't have dragon nails or anything crazy. I still type, game and actually work with people. My nails are just longer than the sports length.