I've run waterjet tables and routers. Between the two, routers are the best choice for a sign shop because of how many different things you can do with it. A waterjet is a cutter, and a cutter only. They're also messy (the mud/sludge created from cutting with an abrasive has to be shoveled out of the tank periodically and you have to do something with it), and they're hot as all get out in the summer time (they generate steam). They also require a bit more maintenance than a router table.
On the plus side, they can cut materials that routers have trouble with- like steel (stainless or not), stone, tile, fabrics (though your table/tank would need cleaning first), etc.
Still, from what you're describing, my .02 is that your best bet is the way you're doing it. If you go with a router (and, honestly, you seem to have made up your mind that you are), yes- you'll have to wipe off the cut pieces. Yes, figure on it taking 1 minute (give or take) to cut each part (that number includes loading sheets on table, cutting, wiping down, removing cut pieces from table, removing scrap from table, repeat). In an eight hour shift, the table will be idle 45 minutes to an hour and a half for this processing, so figure on 300 cut parts in a day- once the operator knows what they're doing.
As far as what brand, I'm partial to Multicam. Avoid Biesse at all costs, and avoid any company that doesn't offer local tech support.
