With the deprecation of the count() and command users will be asked to move to the use of countDocuments() and estimatedDocumentCount() helpers.
The deprecation messaging in the api and deprecation warning should mention the restrictions on using the following commands/operators in the query/filter of the count and the countDocuments helpers.
restricted -> replacement:
$where -> $expr
$near -> $geoWithin with $center
$nearSphere -> $geoWithin with $centerSphere
Also note that $expr requires MongoDB 3.6+