Does anyone know if linux kernel run by RouterOS exposes necessary interfaces for apps to use hadrware accelerated encryption?
I'm planning to run an alpine container with strongSwan on AX3 (arm64) and would like to avoid obvious misconfiguration in that regard.

If we're talking about AES, just search "linux arm aes instructions" on Google eg

https://www.linaro.org/blog/accelerated ... ux-kernel/

Indeed I'm aware that an implementation is available for the CPU used by AX3. But does "it just works"?

It should. At the end of the day, a container is just another process(es) & Mikrotik only restricts root-like permissions and raw network interface, everything else is largely pass-through.

But to call it "hardware accelerated encryption" is a bit of a misnomer... in reality ARM offers good CPU instructions for it that linux correctly utilize. You'd notice the difference/problem with "hardware accelerated encryption" on the xMIPSx things where there is a separate path for encryption, but they don't support container so not going to come up.