User entities are primarily indexed by profileId + entityType - so the singleton API will scale well no matter how many players you have.
That said, if your use case gets more complicated, with say hundreds of entities of a particular type per user (say maybe you are modelling user created towns, that sort of thing) - you could consider using Owned Custom Entities instead. You can define addition, custom indexes for those... keeps those lookups fast and efficient.
In addition, if you end up having >1000 Global Entities, you should definitely look at switching to Unowned Custom Entities. Same deal - you can define your own custom indexes...
Hope that helps!