I've noticed a bunch of exits that are fly only don't show up until you have fly cast on you. Dunno if thats supposed to be the case:

Dregjur Storehouse

Barrels are torn to pieces, the remnants haphazardly thrown across the
room. You highly doubt anything has been here in the recent past - a thick
layer of dust coats everything in the room. A gaping hole in the center of
the floor leads to another room below you, but you doubt you could climb
down without hurting yourself. The hole appears to be getting bigger as
the floor collapses, so you had best be careful.
Obvious exits: out.

(149 H 34 M 1086176X): sn down
You must fly to go that way.
(149 H 34 M 1086176X): c fly
hide
You can fly!
(149 H 19 M 1086176X): You attempt to hide in the shadows.
You slip into the shadows unnoticed.
l
(149 H 19 M 1086176X):
Dregjur Storehouse

Barrels are torn to pieces, the remnants haphazardly thrown across the
room. You highly doubt anything has been here in the recent past - a thick
layer of dust coats everything in the room. A gaping hole in the center of
the floor leads to another room below you, but you doubt you could climb
down without hurting yourself. The hole appears to be getting bigger as
the floor collapses, so you had best be careful.
Obvious exits: out, down.

It's designed that way. If you aren't flying, you dont see the exit.
This was done because most "fly only" exits are set to hidden anyway. Why set
them hidden? Just do it this way, and if you fly you see it, if not, you dont.