Some of my sims in my town ( Bridgeport, Late Night ), are friends with my main sim. However, when I try and locate their houses on the map, they don't show up. I thought it might just be a glitch on my map view, so I went to "Edit Town" to look inside every apartment/house for a certain sim that I was friends with. They didn't show up in any of the lots either. I know for a fact that the sim isn't homeless, because I have a setting switched on that "runs homeless out of town".

Is there any way for me to teleport that sim to my house?
How do I locate the sim?

The mod that will help you cut through all of this if you don't already have it is NRaas MasterController. Its Focus command, run on City Hall or an in-game computer, will bring the game camera to where the sim is if they are actually on the map and not hibernating off the screen as homeless NPCs tend to do. The MC > Sim > Status commands will tell you more about the sim by name such as their career and household status. The Invite Over command will bring the sim over to where your active sim is at the time pretty forcibly once they have time to navigate across the world to them, and provided they aren't gong to get pushed to go to work or school at the same time or they aren't busy doing something of higher priority such as giving birth or dying.

Run Homeless Out of Town is an Overwatch option and it only targets unassigned homeless sims. It does/should not be touching Service Sims who are actively occupying a service position nor Role Sims or homeless co-workers who have a valid reason to be in your world. You cannot have a TS3 game without some homeless sims, and it is still possible that your friend might be one of them.