This is two seperate points your erronously putting together.
First, blade in the dark; At this point in the MQ you dont get random encounters by design. Delphine tells you exactly where the next attack is, so therefor they cant be anywhere else. Once this quest is done, you have to move it on to the initial part of the next part of the MQ ~ diplomatic immunity, before random dragon encounters occur again and it may take some time to do so.
Secondly, dragon souls; When killing a dragon at a word wall site, respawned dragons will not give souls. However if the respawn dragon is a higher level version it WILL give a soul. So for example if you killed a "Dragon" and it respawns as "Dragon" again it wont give a soul. But if you killed a "Dragon" and it later respawns as "Blood Dragon" or similar it WILL give a soul. Only when the respawned dragon is of a higher version will a new soul be granted.