Update FATES LUH and LU x PFT missing value checks

[glemieux]

Task description

Update the missing value checks in FATES to use -999 instead of NaN.

[glemieux]

Note that this was updated to check for both NaN and -999 per a request from @ckoven. This is to allows users that are utilizing an older, but still valid, fates land use data set to continue to do so even though there will be NaNs present.