You assign a property on the Collection here, not on the model, this is why the assertion fails:
$deposit->nome = 'armando';
If you want to work with a single model instance, then use your factory to create one:
$deposit = factory(Deposit::class, 1)->create(); // returns a Collection
$deposit = factory(Deposit::class)->create(); // returns a Model instance
Here is the correct test implementation:
public function testUpdate() {
$deposit = factory(Deposit::class)->create();
$deposit->nome = 'armando';
$this->post('deposits/' . $deposit->id_deposito, $deposit->toArray());
$this->assertDatabaseHas('deposito',['id_deposito'=> $deposit[0]->id_deposito , 'nome' => 'armando']);
}
In the case of the delete scenario, you are making a GET request to destroy a resource, the correct implementation (assuming RESTful actions and you are not sift-deleting!) should be:
public function testDelete()
{
$deposit = factory(Deposit::class)->create();
$this->delete('deposits/' . $deposit->id_deposito . '/delete');
$this->assertDatabaseMissing('deposito',['id_deposito'=> $deposit->id_deposito]);
}