I'm about to turn part of my metal barn into a woodworking workshop and was considering raising the floor (from concrete) to allow for an easier on the feet/legs to approximately 6" (2x6) and running ductwork underneath for dust collection piping. I'm uncertain about the type of dust collector I will use and whether I want it physically in the workshop itself. If I place it in the barn area next to the partitioned wall, then I may have to contend with field mice getting through & into the raised flooring area. I considered the overhead ductwork but don't want that in my way. My floor surface area will be 28'10" by 20'. I'm also concerned about the noise levels of the dust collector itself IF I place it in the actual workshop; are they quiet enough or would you have to wear ear protectors all the time. I'll probably end up with a maximum of 5 or 6 machines connected to it (plus a sweeper port). Any suggestions? Also, IF I go underneath, is it advisable to secure the flooring with screws instead of nails for access to the ductwork at any time?

Yes, you will want it inside, other wise you will pull all heat and cooling out of the shop. The noise level will not require hearing protection but could be annoying. The ideal would be to have it in an enclosed area outside with a return air vent back to the shop. Also make the emptying of saw dust easier.

If you can, go with 2x8 joist, some of your piping will probably be 6" diameter. It is the volume of air flow, not the low pressure that matters. Install flooring with screws. You are bound to get a blockage sooner or later. I think I would go with 4x4 sections of plywood flooring. When you get to the stage of purchasing you system, consult with the manufactures rep. Many offer design services with a refund if you purchase their system.