What exactly is the difference between = (drone) and # (riff)? Define!

I can't. One definition of drone could be: it's pretty safe for harmonic mixing. Riff, on the other hand, can be tricky even when mixing tracks of the same key. It's difficult to explain, but when you practice a lot, you'll end up knowing what riff is.

I think the notation is very fuzzy and ambiguous.

It is. But there's a good reason. If DJ notation was software-engineer precise, it would take a lot of time and effort to learn. It just wouldn't be intuitive enough. Since the notation's main purpose is to record the tracks overall composition, it needs to be very simple. Btw, any effort to write music into notation is destined to be imprecise.

What about harmonic mixing? Does DJ notation take it into account?

Yes, DJ notation was developed with harmonic mixing in mind. See harmonic mixing section for more info on how you can leverage both.

Can I use DJ notation in my commercial product? Can I put it alongside the tracks in my music download service?

Yep. I'd like that very much. The notation is Creative Commons (CC) licensed.

Are there any other DJ notation systems?

Yes, there are, but not the same kind as this one. You can find a lot of different scratch and turntablist notations around the internet. But as for writing down dance music composition, I haven't found anything similar. If you do know about something similar to this, do tell!