You lose deer when you settle on them?
I had a game where I settled on horses and I definitely got the horses after I settled.
Does it depend on if they are luxury or strategic resources?
= Assuming its a grassland horse =
You don't lose the horse or stable bonus. But you change the 2F1H (horse) tile into a 2F1H (city) tile. If you settled on a grassland tile instead, you change 2F to 2F1H, so you get a bonus H by not settling on the horse. Same for any luxuries.
So lets say you have to choose between settling on a grassland horse or an adjacent grassland, do this mental calculation:
Settle on grassland:
City: 2F1H
Horse: 2F1H, 2F2H with pasture, 2F3H with stables, 3F3H after fertilizer
Total: 5F4H for the two tiles in question
Settle on horse:
City: 2F1H, 2F2H with stables
Grassland: 2F, 3F with farms, 4F after civil service/fertilizer
Total: 6F2H
The total yield from settling on the grassland will be higher, but will have 1 less food. It depends on what you want more, food or hammers.
Now lets look at the OP post:
=assuming you don't steal the Mombasa land=
Settle on Deer:
City: 2F1H, 3F1H with Granary
Salt: 3F2H1G with mines
Cotton: 3F3G with plantation and fertilizer
Total: 9F3H4G
Settle on Cotton:
City: 2F1H2G
No Salt but we will have to use this citizen to work lets say a farmed grassland hill: 2F2H
Deer: 3F2H1G with Granary
Total: 7F5H3G
The difference is not big.
But I would settle on Deer just because you can steal Mombasa's land