What have people been using for Yubikeys as an alternative? Installing safes onsite and self monitoring?
If you can't do the monitoring, and you face very advanced attackers like this, it's probably best to only use a laptop that you physically keep with you at all times, and then you can keep your Yubikey with you at all times too.
If you just want to protect against an attacker sophisticated enough to steal a Yubikey but not enough to install malware, then maybe instead of a second Yubikey in the safe deposit box, you could have an encrypted recovery code in the safe deposit box, and either memorize the password, or store the password on your computer.
I've never heard of attackers stealing a Yubikey though. More likely is the attacker will social engineer the website's support into giving over your account.
(And if you actually need to worry about things like that, then you've got (or should have) people who think of things like that for you)
Frankly your main threat is probably a fire or flood. Not a Russian agent breaking into your house.
A couple of years ago, I had my wallet fall out of my pocket while I was on a boat.
My phone was back at the dock safe and dry so I had my primary authenticator. And I probably had printed copies somewhere at home.
I've been much more diligent since then about making sure there are copies and that they're accessible.
You should align your storage choice to your contingency plan. For a lost root your contingency plan should involve distrusting and replacing the hierarchy underneath the root. To the extent that you wish to avoid executing the plan, buy a better safe so you are less likely to need the plan.
It is OK for your contingency plan to include "Go bankrupt and cease to exist" if you are any sort of corporate entity.
"Installing safes onsite and self monitoring" was literally the example given by the person asking for other suggestions.
In any case, the issue of securing something that you only want to use in extremely rare cases is still an issue—"nowhere" isn't a solution to that problem, although I can see the argument that hardware keys aren't the best choice of storage medium (although as an efficiency measure it could be useful to have one in there as well so you can go quickly if it works).
It is also sometimes in your interest to get things in the custody of an individual, ideally your attorney. If the owner of a deposit box becomes aware of your death, they will seal it until a court order is obtained.
My aunt was a hoarder. At that point, I was actually relieved that the box was empty and I wouldn't have to go through the process of claiming the contents.
My aunt was also somebody who bought gold and silver, something that was promoted heavily to people in conservative Orange County California when Obama became president and end times were near. Chase made it very clear that I was basically storing things at my own risk. I could deposit US coins from the 1880s at face value of $20 and get FDIC insurance. Instead, since they were about $1200 each at the time, I put them in the safe deposit box.
Before that, in Oregon, my dad died but I was on the list of people allowed to use the box so I had access. That might be an option if there's somebody you really trust.
The banks do charge about $100 to drill the lock if you lose the keys. It's possible that you could have somebody authorized to use the box but not give them a key.
It creates problems when folks store their wills in the box!