How can I count the students on mongodb
Try the following: 

db.etudiants.aggregate([
 {
   $unwind: '$cours_reussis'
 }, 
 {
   $match: {
       'cours_reussis.note': {
           $gt: 60
       },
       'cours_reussis.nom_ecole': "ENSA"
   }
 }, 
 {
   $group: {
       '_id': {
           'nom': '$nom',
           'prenom': '$prenom',
       }, 
       'num_courses' : { "$sum" : 1 }
   }
 }, 
 { $match : { 
      'num_courses' : { '$gte' : 3 }
  }
 }
])


Does this meet your criteria?

Note that the only changes I made to your aggregation were the following: 


I limited the '_id' to just the 'nom' and 'prenom' fields 
I used $sum to count the number of completed courses 
The initial $projection stage was removed, as the aggregation can perform this optimization automatically.