Lol like I said **** logic. Its the same thing with Madara using Kamui. Logic doesn't seem to matter to Kishimoto at least not when it comes to Madara. He can break any pre-established rules with no explanation necessary.
I'd like to make a reason why it's logical but I can't think of one. I've thought of same as you, maybe once you unlock susanoo you can use it even without your eyes, but that doesnt make sense and MS eyes slowly seal themselves until you cant use them anymore at all.
Maybe it's because he had EMS? IDFK.
IDK for sure either about the Susanoo.
Maybe EMS has different rules yeah.
Maybe because the eyes were open but not in his own eye sockets, yet linked.
One eye open in Obito, the other eye open in some place where Obito hid the eye.
Just as Kakshi's sharingan went into MS together with Obito, even though they were in different eye sockets. They could see through each others eyes even (as kids and during the war as adults, when one was in Kamui and one wasnt).
But really I cant give a for sure answer on how Madara used Susanoo with empty eye sockets.
On the other hand it doesnt bother me much though.
Maybe because I dont see it as something that Kishi cant explain later.
Doesnt seem hard to come up with something for Kishi for things like these.
One can theorize about some possibilities of why as well, that could seem plausible.