That's not why a lot of software is lost. A lot of software is lost because nobody bothered to back it up. There are many ways around not being able to run a program on modern Windows.
Now days you can't back up someone's software, even if you want to. ( Because of DRM and cloud.) And problem will only get worse. To prevent software entropy and rot it should be built on healthy foundation.
With the exception of cloud gaming (which is a particularly nasty thing for preservation), fortunately people still back them up anyway. It's not ideal because cracking is not a 1:1 binary in a preservation sense, but fortunately in many cases the original media can be backed up 1:1 and any necessary crack can be distributed for separate installation. Even if a pre-cracked version is the only thing that survives long term, it's still better than nothing.
What about with wine? I haven't tried, but could old 16bit apps run in wine on windows x64?