Thin doesn't know or care about the Apache configuration. It only adheres to its own config and will only spawn 2 servers as a result.
The reason every third request was kinda slow is probably due to Apache rerouting the request. Since the two thin servers are using ports 6000 and 6001 the reference from Apache to port 6002 cannot reach a server - the port is simply not used by any.
Apache still tries sending the request there, because it also doesn't know if there's a server behind that address/port. It then waited for a timeout (a few seconds?) since no response was given and then rerouted the request to one of the other ports (6000 or 6001).
Apache doesn't "save" the unreachable server because it might just be a temporary outage. You can probably change this behavior with some settings (at least that is possible in Nginx)
You should either remove the third port definition in Apache or add another thin server.