Yes. If a CI is discovered by more than one UCMDB and the data between the UCMDB's is then synced, more than one licences be used.
For example, if a CI is discovered by two UCMDB's and the data between the UCMDB's is then synced, two licences will be used - one on each UCMDB where the CI is discovered. To avoid two licenses from getting used, the IP ranges of the machines must be aligned so that if an IP is a part of the IP range of the first UCMDB, then that CI should reach the second UCMDB only through integration.
This works on UCMDB 10.11 Cup6 and later versions.