How do I update the Menu Icons of new Numix icons? Well, there are some apps, they don't have a own numix icon, but I've seen, that Tilda, Master-PDF-Editior and I guess some others meanwhile does have their numix icon. But they don't change the Icon to numix style. By the way, I use Numix icons since I have installed Ubuntu Mate 14.4 in last December. For example you see here the apps variety and master-pdf-editor.
Mmmmh, okay, you can try looking in the "Pixmaps" folder and see if you can edit anything that way?:
File system > User > Share > Pixmaps. Basically, right click an icon > properties (put it on the desktop first) and then click on its own little picture which is top left, then select pixmaps on the left of the home folder tree at the bottom!.
Your second Tip has been very much better! Thank you for your fast and constructive help! I appreciate this really! Now I have a full Numix Theme how I desired it. And my customizations survived a first reboot. I hope they will do it for future (updates are exepted).
Of course a screenshot as well with my optimization: