Yes, you can tell if a system head is being used. There is a distinctive profile, particularly with how the nose meets the face, that can be observed. You can still make a system head look nice, but there is a clear difference between the two. Many people elect to start with a mesh body and update to a mesh head at a later time. The problem with this has been getting a skin that will work to make the transition. It's possible though, with BOM implemented to use a system skin for the face and body, to do this.
One thing to keep in mind too if shopping for a mesh head is that there are standard mesh heads and bento mesh heads. Most places do bento, but there are some regular mesh heads still floating around. Make sure yours is bento, for the best customization. Bento costs more typically, but allows you to use the sliders to change the bone structure of the head, just like a system head.