It's still in your configuration in the properties files.
Depending on your configuration (I have an out of the box 3.1.1 assembler service locally), the assembler service runs out of the following folder:
...which has a WEB-INF folder containing a number of configuration files. For the MDEX Host and Port, you can open assembler.properties and see it right down towards the bottom.
Hope that helps,
Lots of options here. Two off the top of my head:
1) Separate instances of the Assembler service per Application. If your sites are very different (different cartridges deployed, different URL structures, different SEO strategies), this would be the way to go.
2) Front the assembler with a servlet and extract something from the request (a key, a name, the host and port itself) and use that information to initialize the MDEX Request.
You also might be able to declare multiple mdexResource beans and use Spring configuration to get what you need.
Note: I'm assuming you mean that you have different web apps here. If you're talking about N MDEX Engines that serve 1 site for load purposes, use a load balancer and point the properties file at the load balancer and you're done.