There is no such clause in the North Atlantic Treaty, and many NATO members (including founding members) were admitted with territorial disputes, including with other NATO members, either admitted earlier or simultaneously admitted.

NATO members are required to pledge to resolve disputes of any kind in accordance with the principles of the UN, endeavouring to do so by means which are both peaceful and not disruptive of international peace and security, but without prejudice to any of their rights under the UN Charter including those of individual and collective self-defense, and to declare that at the time of their accession to the treaty none of their existing "engagements" violate those principles. (See, particularly, Articles 1, 7, and 8 of the North Atlantic Treaty.)

There is no reasonable reading of the Treaty which would prohibit a new member from being admitted while while some of its territory is under hostile occupation or while engaged in a defensive war on its won territory against an aggressor; it may make it more difficult to achieve the required unanimity, but there is no "territorial disputes clause" preventing it.