In our current campaign, I created a type of "ancient magic" that does not require an item be masterwork in order to be magical and since it is non-standard magic, it also does not detect with Detect Magic.
It has added a new dimension of thinking to the players because any run of the mill item can now be magical and the only way to find out is to use the item (course, these types of items are rare, but because of another aspect of the campaign plotline, the PCs have found one such item so far by 3rd level).
I became bored with the repetitious concept of:
1) Find masterwork item.
2) Cast Detect Magic on it.
or
1) Cast Detect Magic over everything.
Another thing one might do is require a successful Appraisal roll to find out if an item is masterwork in the first place, but blanket Detect Magics over all found treasure foil even this (shy of items that have innate Nondetection spells within them).
In response to the OPs question, since Invisibility detects as magical, Nondetection works well in conjunction with Invisibility (assuming a DM does not use a extremely literal interpretation that Nondetection protects a creature's gear, but not the spells on the creature).