In The Great Gatsby, what indication is there that Tom and Daisy are closely linked despite their marital difficulties?

In answer to your question concerning Tom and Daisy in The Great Gatsby, I suggest that there isn't much indication that Tom and Daisy are closely linked. 

The only bit of evidence that they are, occurs when Tom mentions a few good times they once had and Daisy is convinced that she did at one time love Tom.  She refuses to announce, as Gatsby wants her to, that she never loved Tom. 

This is hardly conclusive evidence of how closely linked they are.  All this amounts to is that Daisy wasn't pining for Gatsby the last five years like Gatsby was for her.  That's the point in this scene. 

Tom and Daisy have a terrible marriage.  They do not respect each other, they do not communicate in any meaningful way, they both have affairs.  In a time of stress they choose to maintain the status quo.  And Daisy, showing her realism and character, refuses to pretend that Gatsby's illusion is true when it isn't.