I guess that I'm just repeating what everyone else has already said, but yes, if you are using your batteries heavily then they will get warm (or hot, depending on the load).
But the lower the internal impedance (resistance) the less hot they will get for the same amount of supplied power. NiMH have lower internal impedance than alkaline batteries and should cause less heat and faster recharging of the SB800.
Lithium Ion batteries have the greatest charge density (per volume and weight), but they also have higher internal impedances than NiMH or alkalines and, while they will last a long time, will not charge a flash as quickly as NiMH.
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