Ok, it’s reproducible in my 17.04 VM… I’ve changed the position in panel prefs dialog and then used killall mate-panel to restart it, and nm-applet wasn’t there. Before restarting, the whole tray area wasn’t visible, I suspect it was somewhere below the screen - but it’s a VM, so I’m not surprised. 
Also making the left panel wider doesn’t help. Moving it back into bottom does… nm-applet reappears.
I’ll tell our developer, Colomban Wendling, about it. He’s the author of SNI support for tray area, and he also fixed the bugs there - so actually it’s him who should be thanked, not me