Dear Justin,
Do you have counts of missionaries by city? Or by country?
No one has counts of missionaries by city (or by province, for that matter). For one thing, security issues would make this almost impossible to gather (can you imagine trying to collect counts of missionaries for, say, Kabul, or Peshawar, or even Beijing?). For another, there are simply too many cities.
Part of the problem with collecting counts of anything for large data sets is that there’re just too many places to count – unless the people in each individual place collect the data and report it. This is why we can know a lot about the traffic, stock, and revenue of individual Walmart stores, for example, but we can’t know how many missionaries or aid workers or whatever are at work in individual cities.
Another part of the problem with collecting counts is that they change all the time – even inside the same year. Take any given church: the number of people who attend Sunday morning service at Christmas time is vastly different than those who attend in June, for example. Members change, too: babies are born, people leave, people join. The number of members of a church (or missionaries in a city) at the start of the year can be very different from the end of the year.
Missionaries by country have been collected in the past – there were numbers in the 2000 edition of Operation World (OW), as well as in the 2nd edition of the World Christian Encyclopedia (WCE). Two hundred and fifty  countries are easier to count than thousands of cities. Still, security issues being what they are, the number of missionaries in a given country is also a sensitive number (though it can be easier to collect than in cities). There was no count in the 2010 edition of Operation World, and security was certainly one of the reasons for this omission. Some researchers think the count in OW2000 may be the last published accounting – if not forever, then certainly for a very long time.
The missionary numbers, even by country, are estimates, for the same reasons as cited above. But there’s one other thing I’ll throw in here: put simply, how we define ‘missionary’ makes it difficult to count. Long-term workers? People there more than 2 years (the MARC Mission Handbook definition)? Short-term workers? BAM/tentmaker types? Teachers? Getting numbers from the ‘big’ mission agencies is hard enough: there are thousands of small ‘mom & pop’ agencies, not to mention the non-Western agencies that rarely report, present as well.
In fact, the World Christian Encyclopedia’s approach – estimating the per capita missionary count – may be the only realistic way and most accurate way to do it. (Just don’t compare WCE with OW, at least not directly: WCE counts Catholic and Orthodox missionaries, while OW does not…)