How can we consider the present Kashi Vishwanath temple as a Jyotirlinga when the original temple was already destroyed and the original lingam too is untraceable?

Kasi itself has vibrations. Visiting Kasi itself sufficient to worshipping original lingam.

South has a tradition of visiting Kasi in one’s lifetime. This will be followed by visiting Rameswaram, another Jyotirlinga.

Rameswaram has two lingas.

 One is constructed by Sita Devi, called Ramanatha Swamy and another brought by Hanuman from Kasi. 

Though main deity is Ramanatha Swami, you can find Kasi Viswanath adjacent.

Another Temple in Then Kasi (Kasi of south) for those who cannot visit Kasi on banks of Tamira Bharani in Podigai Hills.

South has two lingas from Kasi, one by Hanuman and another at Then Kasi.