SELECT 
  products.company_id, 
  COUNT(DISTINCT products.product_id) as products_count 
FROM 
  cscart_products as products 
  LEFT JOIN cscart_companies AS companies ON companies.company_id = products.company_id 
  LEFT JOIN cscart_product_popularity as popularity ON popularity.product_id = products.product_id 
WHERE 
  1 = 1 
  AND companies.status IN ('A') 
  AND (
    products.amount > 0 
    OR products.tracking = 'D'
  ) 
  AND products.status IN ('A') 
  AND (
    products.usergroup_ids = '' 
    OR FIND_IN_SET(0, products.usergroup_ids) 
    OR FIND_IN_SET(1, products.usergroup_ids)
  ) 
  AND products.status IN ('A') 
  AND products.parent_product_id = 0 
  AND products.company_id IN (799) 
GROUP BY 
  products.company_id

Query time 0.09391

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "companies",
          "access_type": "const",
          "possible_keys": ["PRIMARY"],
          "key": "PRIMARY",
          "key_length": "4",
          "used_key_parts": ["company_id"],
          "ref": ["const"],
          "rows": 1,
          "filtered": 100
        }
      },
      {
        "table": {
          "table_name": "products",
          "access_type": "index_merge",
          "possible_keys": ["status", "idx_parent_product_id"],
          "key_length": "4,3",
          "index_merge": {
            "intersect": [
              {
                "range": {
                  "key": "idx_parent_product_id",
                  "used_key_parts": ["parent_product_id"]
                }
              },
              {
                "range": {
                  "key": "status",
                  "used_key_parts": ["status"]
                }
              }
            ]
          },
          "rows": 4670,
          "filtered": 100,
          "attached_condition": "products.parent_product_id = 0 and products.company_id = 799 and (products.amount > 0 or products.tracking = 'D') and products.`status` = 'A' and (products.usergroup_ids = '' or find_in_set(0,products.usergroup_ids) or find_in_set(1,products.usergroup_ids))"
        }
      }
    ]
  }
}