Yes, you can delete the runways that are not in the theater with no negative impact. You won't miss them unless you tried to write PTO missions in Mission Builder from your MTO install, not likely.
The runway numbers (runway.1, runway.2, etc.) must be in sequential order for them to show up in your MTO Mission Builder. If not, those from the break in sequence on won't show up. I don't know a shortcut way to mass edit them, you'll need to do it by hand. If the ID numbers (id=9640, etc) are out of sequence that is OK.
If you never plan to use the Mission Builder in your MTO install then it doesn't matter. You don't need to change anything. The airbases.dat file is used in Mission Builder, not in flying missions, campaigns, or Free Flight. As long as the individual airbases are installed properly they will show up in your missions regardless of what is in the airbases.dat file.
