I used to work on the "connector department" for a large (no.1) telecom radio access supplier. I never tell anyone so they don't keep me from doing fun stuff instead of connector selections! ;)
There are in fact a lot more than USB and audio jacks that can handle this 1000 cycles you're asking for. Even a battery powered drill might have them. So why don't you see connector products advertising 1000000 mating cycles everywhere?
It takes time and money to prove that it can handle the mating cycles specified. A connector product might handle 100000 mating cycles but stating that it does, binds you to it. Stating that you have a USB compliant connector would imply that it can last the mating cycles stipulated by the standards. It's actually quite a lot.
As I wrote in the comment to your question, the Hirose 3800 series is good for 20000 mating cycles, it doesn't mean it's different from a simple pin header (OK maybe...) but Hirose has tested it and can say it works. If you go to Samtec they have plenty of connectors that are "Extended Life" product. It's the same metal with gold plating as everything else, but it's proven to be working for a lot of cycles.
I think that the easiest way for you to obtain the connector you want is to contact a couple of connector manufacturers and ask them which product would be suitable. Of course volume (money) comes into play here. If you're a big company sourcing a lot of products you can just ask and it will be given to you. Low volume gives less support, less commitment, then Google is your friend.