Unfortunately exchanging the motherboard hasn't changed anything. The server is still unstable, though I must say, it hasn't hung, the only problems were the COM port that stopped working and kernel messages about a stuck process on one of the CPU cores.
I've run a memtest too. All RAM working without errors.
In syslog I see the stuck process is always smbd (the Samba daemon). For now, I've stopped Samba, but that still doesn't answer the question why the COM port stops working and what is the cause of the stuck process (hardware, like the SAS controller or one of the SATA hard disks, or software, which had been updated several days before the problems began, so it is strange the server was stable for several days before the problems started). For now, I'm a bit at a loss and don't really know how to proceed further.
Maybe the CPU is the culprit? I will probably have to run some stress tests to try to find that out.
To be continued, that's for sure.