Will 1000 players be enough? I feel like you'll hit the limit by this time next week -- if not tomorrow (I signed up).
I understand that 1000 players will be a lot for you to handle, but that being said, if this thing seriously catches on, you'd be completely justified in charging $1 per month recurring, and I would definitely pay it for the increased density of spies in my area.
Seriously consider making a recurring charge, asap, before it's too late. I made a reasonably successful game where the income was based entirely on new users paying in. It was very difficult and discouraging to me to see my game taking off with unexpected success, while my income stream was totally flat. Server load and personal workload for me increasing each month, while my income was totally the same each month. When the income is based totally on growth, that's what success looks like. Active user count double what it was last month, income same this month as last month. And it doesn't feel entirely good. You need recurring revenue. If you figure out how to provide value, the customers will pay.
Automation can help with routine things, and in areas where you have high density you can effectively have spies create missions for other spies: one person's mission is to take a picture and deliver it with a note for the next person, the note tells them their next mission, and so on.
For added fun, check things like Twilio and their telephony APIs. Phone calls and text messages can add a layer of realism.
The holy grail, as seen in Halting State, is to procedurally generate all the missions, so you get something like:
SMS text to player 1:
Go to place X at midday, write code 12345 on the ground in chalk.
SMS text to player 2:
Go to place X at midday + 10 minutes, reply by SMS with the code you find.
If you have sufficient density of spies, arranging that kind of interaction should be fairly easy. On the other hand, everyone that doesn't live in a large city with an active population in the game is going to have a more abstract experience - no finding secret messages other people have left!
One way to get around that is to find live online webcams - traffic cams, for instance, with a good enough resolution - and get the spies to leave something visible in front of them. Player 2 then just has to locate the area on the web, and view it through the cam.
I understand that 1000 players will be a lot for you to handle, but that being said, if this thing seriously catches on, you'd be completely justified in charging $1 per month recurring, and I would definitely pay it for the increased density of spies in my area.