In general this is a cost issue - hand crafted, unique, un-hackable code written by ubergeeks costs money - much cheaper to use MS based apps to run everything. You can blame the taxpayer who wants less council tax and VAT, cheaper booze, fags and petrol for that one - the cuts have to come from somewhere and defence is, and always has been, a classic target.
Remember that these systems are not accessible from the internet or even the MoDs own intranet, comms are with highly secured stand alone systems ashore. It doesn't even talk to the network I work with onboard, which is for office automation and general pupose use.
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