Just in case anyone cares, I took apart one of the door enclosures on my '98 GS400 and like Percy said, they are ported. The hole is the opening for a channel.

DPGS430: Is that MDF sealed around the edges in any way? I can't tell from that photo but it looks like there's some white foam like sealer around it...

 

I used 1'' wide weather stripping to seal off the MDF. Sure wish I could get my MW170's in the doors...

 

The stereo shop finally put the Boston 5.5’s in the doors. They took out the enclosures completely and used a MDF wood front. The entire job was $45 so I’m not complaining. The sound is much cleaner and gives me a chance to fully test the PPI PCX-480 amp. They said since the speakers are sitting back from the grills the sound may be slightly hollow. I really can’t hear it but they said I could use packing foam to put in between the door and around the speakers. Anyway, thanks for all the info!

 

You can use packing foam, or some of the various types of weatherstripping or air conditioner foam commonly found at Home Depot. Worked well for me.