Hello Tamas,
the exact answer depends on the platform you are using.
On IOS devices the MTU is not the OSI L2 MTU, but as you have noticed you need to increase the mtu with the mtu command before you can use the ip mtu 1588 command.
On the other hand in IOS XR the mtu is actually the OSI L2 mtu so it does include the 802.1Q tag (4 byte).
My suggestion is to accomodate for the 802.1Q header in any case as you are going beyond the standard OSI L2 MTU for ethernet that is 1518 byte without tag 1522 byte with tag.
If you notice in IOS devices the 4 bytes of FCS are not counted in L2 MTU so in show interface command you will see 1514 byte and not 1518.
So I would use a value of mtu 1588+18 byte as minimum in order to be able to issue the ip mtu 1588 command.
Hope to help
Giuseppe