Taking every scanned file is 200kb, can't see you getting much better compression and still being able to read it. That would mean 500@200kb=100mb per working day = 25GB per year + you really need to back this up. So what you need then is a naming convention that relates to the records in your delivery database, that they are filed under day month, year, folder system. The problem is when you get more than one person using the system, even software solutions break down.
I don't think there's anything free out there as its quite specialised software that requires a decent customised database. What have you used before as there seems quite a lot of companies that do actually provide what your after.
I take it that its these type of scanners you got as well, flatbeds just don't cut it.