I've never tried it, and I'd be happy if anyone can provide an answer for how to do it, but it seems to me that getting inside the inner workings of mechanisms like auto-updates is not something the designers of those programs had in mind. I'm sure that even if it is possible through a simple measure (like an EXE or a DLL), actually integrating the update will probably not work well because these programs would expect some other programs to call them.
That said, I can think of two options:
1. Shut down or disable the programs and call them yourself (let's say by simulating a stream of mouse clicks in certain locations). If you ask me this isn't good either, because these programs often want you to restart the computer after the update and I'm sure you don't want that in your program. Which brings me to
2. Don't run a time critical app on a computer that's open to outside influence, and that includes managers playing solitaire, people surfing on NI's site, and yes, automatic updates. Don't let the computer be on the network, or at least don't let it be connected to the internet. Have someone run the updates once a week or once every two weeks.
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