I wouldn't say it's frowned upon. It's just... assuming you are not going the container route, then it's basically the same thing that it always has been with any OS before LXC (and after that Docker) became a thing: One machine for multiple applications (bare metal or VM, doesn't matter). Managing and maintaining those without causing too much downtime is a sometimes unachievable task.
Generally speaking: since Docker became a thing, it really doesn't matter which OS you use to run which application from which image type (Linux or Windows, doesn't matter either).
My personal opinion:
- Use a "real" hypervisor as the underlying OS: ESXi, Proxmox, KVM standalone, whatever suits your needs and skills. Why? Because the OS is made for hypervisor tasks. Windows Server or Desktop with Hyper-V may work well with Windows guests, but managing those, especially with multiple bare metal nodes, may be unintuitive to say the least.
- Use Windows as a VM to run a Windows application
- Use Linux as a VM with Docker to run multiple Linux applications
That's how I do it.
Edit: of course nothing hinders you to run Windows Desktop bare metal as a NAS server. That's a perfectly valid thing to do. BUT: Same problem as running bare metal Linux as NAS server: How would you achieve backups/snapshots? I know it's certainly not impossible, but using a VM is many times more convenient. This is the main reason to use VMs.
dot lan. I don't need let'sencrypt. I just ceeate my own CA, my own (wildcard) certificates, and install the CA into all my boxes that I want or need to have certificate verification succeeding.