R&D budgets are separate from game budgets. General and OS applications may fall under R&D.
I'm fairly sure this is not at all true. R&D in their earnings reports has to include game developement (it's called research & development after all). The only things they're listing are, deprecation of property, capital investments, advertisement costs and R&D. No special clarification of hardware/software. In reality I believe their hardware team is quite small and 55 billion yen is a ridiculous amount of money.