"how efficient will be to use a in memory database to store millions of temporary values?" Code Answer
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the problem is sufficiently simple that you really need to just give it a go and see how the (performance) results work out.
you already have an implementation that just uses simple in-memory structures. personally, given that even the cheapest computer from dell comes with 1gb+ of ram, you might as well stick with that. that aside, it should be fairly simple to wack in a database or two. i'd consider sleepycat berkerly db (which is now owned by oracle...), because you don't need to use sql and they should be quite efficient. (they do support java).
if the results are promising, i'd then consider further investigation, but this really should only take a few days work, at most, including the benchmarking.