[Answered ]-Annotate is adding an extra object to my queryset

You want to work with an Exists subquery ^[Django-doc] to prevent joining:

from django.db.models import Exists, OuterRef


def get(self, request, **kwargs):
    user = request.user
    companies = Company.objects.annotate(
        joined=Exists(
            Queue.objects.filter(company_id=OuterRef('pk'), users=request.user)
        )
    )
    # …

For the serializer, you add a joined field:

class CompanySerializer(serializers.ModelSerializer):
    joined = serializers.BooleanField()

    # …