Yes I do on my secondary system as the room acoustics aren't great in the room that system is in, as a result speakers are a bit lacklustre in there. I usually use system 2 with headphones when my wife doesn't also want to listen to my music choices.
Pro-Ject Debut Revolve with 2M Blue, NAD C350 amp, Beyerdynamic DT 770 or DT 990 Pro headphones. Works very well, but yes any defects/surface noise are more noticeable with headphones compared to speakers. It will depend how good your records are really, but even new ones can have the occasional crackle that you wouldn't otherwise notice on speakers.