This is not pretty, but you can split the string on the ':' and compute the number of seconds since midnight. The code below used cellfun to vectorize the code; a for loop could be use and might be easier to understand (but likely sacrificing performance).
testData = repmat({'11:23:23'}, [10,1]);
hms = cellfun(@(x) str2double(strsplit(x, ':')), testData, 'UniformOutput', 0);
cellfun(@(x) x(1)*60*60+x(2)*60+x(3), hms)
You can compute duration so long as events don't cross midnight. If events do cross midnight, things become more complicate. In that case, if you have R2014b, the new datetime/duration functions may be useful. Here is a intro video.
