That's the danger that you get when your main product lives of someone else's main product. I'm the author of InstaDesk, an Instagram client for the Mac, and I've also always assumed that this day would come. This will probably affect me too, but not as hard as web.stagram and the like, since I'm offering several "pro" features that will probably never make it to the Instagram website. My next release will allow the users to use "comment reply" templates, see which comments they've already replied to, download images for specific tags, etc, and much more. All more suited to people who use Instagram to connect to huge audiences (people with several thousand followers, etc).
In the worst case, I'll need to raise prices to account for a smaller niche market. But let's see, it may also result in more Instagram users since it will be easier now to "experience" the network.
I also hope they finally allow user registration on the web. Currently, users can only register from within the iPhone or Android app, which makes it difficult for people to just register in order to follow a couple of friends.
But yeah, since I've kinda expected this to happen at some point, I've been busy in the past months to work on two separate products, that are slowly nearing completion.