Could a datastore hold a table of 1000 tables with 1000 values?

Yes and no. If you go to http://wiki.roblox.com/index.php?title=Data_store you can see that yes, technically it is possible to have 1000 tables with 1000 values but it would be.. well.. extremely unrealistic to do so through Roblox, at least if you are doing it through datastore. That would be 1,000,000 numbers total. The limit max amount on each int is 260000 (or 256 kibibytes) as stated by the Data Limit section. That part seems okay for this by a long shot but... unfortunately.. you can only call a certain amount of data requests per MINUTE. So if you wanted to wait a few minutes and a lot of lag time it's theoretically possible with my understanding. Here is the chart provided to see how many requests you can make per minute.

Gets		60 + numPlayers * 10
Sets		60 + numPlayers * 10
GetSorted	5 + numPlayers * 2
OnUpdate	30 + numPlayers * 5
Sets		10

So, basically, if you had 10 people on the server and you wanted to load 1000 values it would take 6.25 minutes to load and 6.25 minutes to save. Now I could be missing something and this could be a straight up no but I'm pretty sure if you are willing to wait it's possible, just not so sure it's worth it. Just keep in mind ROBLOX uses JSON.

End sentence. I don't think it's really logically possible. Not to mention there will probably be some lag loading this.