I'm far from a battery guru so, FWIW, in my personal opinion...
It can be normal or it could also mean you have an individual specimen that does not play nice with NiMH. Many of the Duracell NiMHs absolutely suck (although some are quite great), so you need to do a few runs with the eneloops before making the final determination here, IMO (those Sanyo/Pano cells are the benchmark of NiMH in the same way the MBP is the benchmark of laptops.) You may see better performance after several deep discharge/recharge cycles (and many good chargers can do this for you with a NiMH break-in feature.)
Presumably due to the lower voltage, NiMH cells do not always play nice with some of the Magic Mouse models in some instances. I have one where I get a low battery warning after just a few weeks of using eneloop Pros...in reality, well over 95% capacity remains, but the mouse seems to get confused by the lower voltage, makes an incorrect estimate, and the UI throws those annoying messages that Apple does not give us the option to disable. I have another Magic Mouse that can run for 3-4 months easily with the same eneloop Pros (it may even run to 6-8 months sometimes as I lose track?) I've always theorized this has to do with the firmware revisions where Apple tried to correct their error with some success.
BUT...even on the Magic Mouse that will easily run 3-4 months, OS X's battery indicator will fall to around 50% within just several days to a week of use. Then, it will hold at that level for an extended period. So even though you are already down to 47%, the actual capacity remaining in the battery could very well exceed 90%, and this is just a voltage-related reading error.
However, even with my Magic Mouse that can run for months on eneloop Pros, OS X' UI starts giving me that low battery warning when way more than 50% actual capacity remains, as verified with my Maha charger (which doesn't lie), and is still capable of delivering the voltage needed to run most other devices for a very long time. Most other devices I own are capable of running eneloop Pros much lower, including many higher discharge devices that place greater load on the batteries but do a good job of continuing to operate correctly even as the voltage decreases.
Apple dropped the ball here IMO from both a functional and environmental perspective by failing to design a device and/or device firmware that can fully utilize ULSD NiMH. They did the same with the earlier generation of the wireless keyboards that used two AAs. Eneloops last significantly longer than alkaline batteries in many devices (especially high-drain ones), and, when a device has issues with a high-end ULSD NiMH as such, IMO that is a design failure on behalf of the device Maker. Most devices made in the past several decades don't have this sort of issue.
