Hi Daniele.
For what I understand, on this industrial machine, you have three PCs with OS/2 Warp 4, with network connection (ethernet), and 8 serial ports on each machine and these 8 serial ports are connected to the PCs with ISA cards.
I think it will be hard to VBox to emulate the 8 COM serial ports.
Backup everything. Clone the hard drives of each three machines. (Possible you already did that).
It will be interesting to know why you want to have OS/2 virtualized there over Windows. Is there some functionality that you don't know how to use on OS/2, like using USB flash drives to extract files or VNC for remote control? Or is it that you are missing the OS/2 installer CDs? or is it that OS/2 is different to install?
Possible solutions with bare metal (real hardware) are:
1) OS/2 Warp 4.52. Since it seems you didn't upgrade any of the PCs to newer maiboards (you have that old ISA cards that you need for the 8 serial ports). You can install OS/2 Warp 4.52 from the CD-ROM, get USB support (maybe for a flash drive), and copy the required software for this machine from the clones Warp 4.
OS/2 Warp 4.52 will save you some time with all the fixpacks for Warp 4.
2) Buy ArcaOS and it will save you also too much trouble with the OS/2 Warp installation process and it will install more actual tools and drivers (network). Since it is the same OS/2 kernel is almost sure that every driver and software will run. To install ArcaOS you need a DVD drive, or the capacity to boot from the USB port.
It would be very awesome if you can share the config.sys file (upload it as config.txt) too see if there is any special driver or specific thing for that machine we can point out.
I would love to be in Italy to check out that machine !!!!

Regards