What IR sample rate do I import for Axe3?

In theory, yes avoiding resampling is probably the safe bet. In practice, if the resampling is done well, you'll likely never hear the difference. 96 kHz is exactly double the rate of 48 kHz, so the math there is trivial.
 
Would it be better to use 48k to avoid resampling ? (thinking if resampling would bring something unwanted to the sound)
when the native sample rate is 96k the files are getting resampled one way or another, whether you do so in real time or bake it into the file is personal preference. the resampler in the box is reference quality and cpu overhead is minimal
 
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