Asiya and Shah were already in custody in separate cases while Alam was brought from Jammu and Kashmir on transit remand.
It also alleged that Shah was in regular touch with Hafiz Sayeed, Chief of Pakistan-based banned terror outfit, Jamat-ud-Dawa.
JKDFP, a separatist political party launched by Shah in May 1998, favours tripartite talks involving India, Pakistan and Kashmir's representatives.
The Ministry of Home Affairs (MHA) released a statement following rumours over the health of the separatist leader, lodged in the Tihar jail since his arrest on July 25, 2017.
The court had on February 18 sought response from the Enforcement Directorate on Shah's bail plea.
Pulwama attack fallout: J&K administration withdraws security of five separatist leaders, including Mirwaiz Umar Farooq
Besides the Mirwaiz, the security cover for Abdul Gani Bhat, Bilal Lone, Hashim Qureshi and Shabir Shah has been withdrawn, local police officials said.