Why is checking Android filesystem possibly harmful? I just had an idea to do a filesystem check of all Android partitions when I noticed there is an option to do that for /data /system /cache in STweaks app (which comes also with Dorimanx Kernel) but it warns:

!WARNING! This is a VERY DANGEROUS OPTION![...]

So why is it so dangerous?
It's even riskier than cybersam says. You shouldn't check/repair a mounted filesystem (i.e. when it is in use), on any operating system, because programs might be using the files while you're checking them and possibly making changes. This could cause the checker to think there are errors where there are really no errors; it might cause unexpected behaviour of any program that happens to read or write files during the check; and any files written during the check might be corrupted or completely lost.

On a PC, you can check a non-essential filesystem by unmounting it before the check, or you can check a system partition by booting from a USB stick or CD so that no filesystems from the hard disk need to be mounted. On Android, the closest equivalent is doing it from the recovery: this way, you can check any filesystem other than the one the recovery is on (assuming the recovery doesn't mount the SD card).