A valid question, though it can be interpreted in multiple ways.
Each carrier has it's own ID, so from a game mechanics point of view nothing needs to change, but I'm guessing you are referring to the "physical" location of the carrier in space and how that is represented to the user in game?
Not gonna sugar coat it, as it is the game couldn't handle it in any graceful way: the issue stems more from the way in which carriers are currently handled on the contacts panel than potential issues with clustering carriers in a formation at a specific point; too much stuff in the contacts panel.
A potential solution would be to introduce a new Contact Type to the mix: much like unidentified signals can be resolved into different types upon scanning one could have a "Carrier Cluster (might want a better name for this)" signal that remains unresolved (as far as the contacts panel is concerned) under normal circumstances unless the player makes an effort to scan it down and see what's inside it.
Add to this the ability to automatically resolve Own Carrier + Squad Carrier + Friends Carriers and you now find your self in a situation where you only see the carriers you care about in the contact panel unless you make the effort to search every "Carrier Cluster" contact in the sector.
Also, Bookmarks are always available and should work as they currently do.
I'd honestly welcome this change even if no slots are ever made available: there are only so many carriers an average player actually cares about