This issue can be closed, I have resolved it.
Resolution:
1. Remoting on to the root domain controller with all the FSMO roles
2. Open Adsiedit and open the following "Configuration" and the name of the DC with FSMO roles, after that choose connect
3. Navigate to the following: CN=Configuration, DC=dommainname, DC=com -> CN=Services -> CN=domainname -> CN=Administrative Groups -> CN=Exchange Administrative Group (FYDIBOHF23SPDLT) -> CN=Servers -> CN=Netbios name of the exchange server -> CN=Protocols -> CN=HTTP
4. Here we have most of the data objects that iis (the iis on the exchange server) writes to Active Directory, in our case the whole EWS was missing here.
I am most likely sure this occoured when we just tried to recreate webservicesvirtual directory from the EMS (remove-webservicesvirtual directory / new-webservicesvirtualdirectory).
5. Creating a new dataobject here (msExchWebServicesVirtualDirectory), when creating this object all the mandatory attributes should be written in this data object by default, if not then add them manually. You might need to configure some of the optional attributes as well ( if someone needs to know they can send me an mail or I can post them here when i have time)
6. After this we get a WebServicesVirtualDirectory from EMS (though its a base one, from scratch in other words we need to configure it now but atleast we get it =) )
Regards,
/Juuso