I'd enjoy this too, though for the OpenPGP app (I use gpg-agent for my ssh key, stored in my Yubikey).
I suspect the problem is that the programs have no way of knowing that they Yubikey is waiting for a touch vs. any hardware token just being slow to perform an operation. If this is true, it is a difficult problem to solve, because API (at the OpenPGP Card and PKCS#11 layers) would need to be changed/added, and protocol (at the PIV and OpenPGP layers) would need to be created, and would likely have to go through different standards body's processes.
As a workaround solution, it might be feasible to change the clients using these to timeout after a reasonable time (maybe 5 of the 15 seconds) and display a message asking the user if the token is waiting for input, but that would be at the application layer (e.g. gpg-agent or equivalent when doing PIV based keys, or possibly the ssh command itself). Unfortunately, not something I have time to hack on these days
In the mean time, I'm working on getting my physical setup such that the yubikey is both visible while looking at my monitor(s), and not so far from the keyboard that it is uncomfortable to reach.
