The warning means those partition already had a swap signature, e.g. the
mkswap command was already executed in the past in that partition.
As you executed
mkswap again, it warned you it would be deleting an old signature.
fdisk does not showing it, it does mean the partition is not labeled as a partition device, however it does not mean it is not being used as such.
To put there the code for swap partition, you can do:
sudo fdisk /dev/sda
Partition number: 3
Hex code: 82
- t is the command to label a partition with a code´
- 3 is the partition number
- 82 is the hex code por a swap partition.
fdisk -l will show
sda3 as a swap partition.