Well, basically, it's a little bit of all of those things. With bonds, yes, you might buy a zero-coupon bond at 110 and get 100 at redemption (doesn't necessarily mean you lose money, since, in the meantime, you might be able to fund the bond at an even more negative rate or you might have disinflation or smth).
In general, there's nothing special about zero, so negative rates work the same way as positive ones do, with the a caveat around physical cash. How it all works? It's a little complicated, but if you wanna read a nice note on the subject written by the Bank of England, you can find it here:
http://www.bankofengland.co.uk/publications/Documents/other/treasurycommittee/ir/tsc160513.pdf