5wolves, welcome to the Chronicles Network! I hope you enjoy posting comments and reading the observations of others as much as I do.
"Once they had been six... Four remained..."
To me, this means there were six... Now only four are left (Ghost, Nymeria, Shaggydog, and Summer), but Ghost has a hard time detecting any connection to Summer.
But the strongest evidence to me is the lack of information regarding Lady in Eddard's, Bran's and Sansa's POVs.
If Eddard did not kill Lady... If Eddard deceived Robert... If Eddard had a secret to tell Sansa... then I think this information would have come to us in through either his fevered dreams or through his regrets while he was in the dungeon, especially when Varys mentioned that Sansa would suffer if Eddard refused Joffrey's mercy.
It is Ghost's feelings that give rise to a theory that Lady might be alive. Now Jon's understanding of his connection to Ghost pales in comparison to Bran's knowledge of Summer's feelings. Bran has also pushed his abilities much farther than Jon... to the point of possessing Hodor. If Ghost can sense his siblings, why not Summer? I'd expect Lady's presence to be found by Summer before it is detected by Ghost.
Sansa and Arya were with their wolves for only a short period of time. Their connections were not as fully developed as any of their brothers'. Even so, while Arya travelled the Riverlands she sensed Nymeria. Sansa has been in KL and the Eyrie ever since she lost Lady in the Riverlands. Sansa is not that far from the Riverlands... I think she'd have sensed Lady.
As for Lady's significance to Sansa...
How much of Lady's death will be directly applicable to Sansa? Will she be killed by a family member? ...a person she trusts? ...the Hand of the King? ...the Lord of Winterfell? Will she stare straight into her killer's eyes? Will she willingly submit?
Compare Lady's death to that of Nissa Nissa, wife of Azor Ahai. Nissa Nissa apparently willingly allowed Azor Ahai to plunge his red hot sword straight into her heart. She trusted him. She probably looked him right in the eye.
Could Sansa Stark be the Nissa Nissa to Azor Ahai reborn?