That is a really good intuitive question my friend.
When it comes to cloning with these little net pots, it more about what the pot does for me than for the plant.
The roots will emerge from those holes once they start, and this is the main reason I use them, visual confirmation holes. Saves a little time and effort instead of planting straight into soil. In the event that a clipping doesn't take, it's more work altogether. I'll take pics of the roots emerging from the holes when that time comes!
Net pots are also used in hydroponics, which is where I got the idea for this use.
That would be great to see. I have a hydroponic set up for vegetables, and the little plastic cups that hold the plant do have openings for the roots. 3D printed cups would be awesome. I imagine little ones printed with the designs for different herbs and vegetables so you can tell at a glance what plant you have (plus social-media ready for photography kicks).