Does continuing to donate past 999 achieve anything?

Related question - What does the donation machine do?

In BoI: Rebirth, you can donate to a machine in the shop room, and as you put in more and more money, you can unlock things.

When you hit 999 coins in the machine, you unlock an item and the machine blows up. I figured that was the end of that.

However, on my next playthrough, the machine was back! So I have dutifully been feeding more money into it. However I'm up to a couple of hundred gold in there now and it doesn't seem to be doing anything.

Am I wasting my money? Or will this 2nd round of donating eventually unlock something awesome?

It won't unlock anything, all you can do is use it as a bank for future runs.

The blowing up was not caused by adding your 999th cent, that was because you got it to 1000 cents.

So in a way you are wasting your money (if you donate money instead of buying stuff anyway), in a way your are giving later runs a potentially bigger chance for buying items (assuming you bomb the machine in that run).

No, you won't unlock anything, according to BoI: Rebirth wiki.

Moreover, it's not recommended to add a 1000th cent to the Donation Machine and make it blow up. That's a huge waste of pennies! Because if you destroy it the machine will only drop a bunch of dimes that you have to use in that run and the penny counter will restart from 0 in the next one.

So it's better to keep the Donation Machine as a penny-bank that exchanges "bombs for money".