Most folks use IEEE floats as their value type, so in a way a whole lot of libraries have supported missing values for a long time. Many languages can use 32- and 64-bit floats; R can only use one or the other (you have to rebuild it to change this). This can make your big data twice as big as it should be. In that, R is in the company of such serious number-crunching languages as Lua, JavaScript, and Splunk.