Storage space is cheap nowadays, so it is usually less efficient to 
send attachments as links. If the same message with attachments is 
sent to multiple recipients on the same server, the message will be 
sent only once and be delivered to the users mailboxes at the 
receiving end. In contrast, if the attachment was linked, each 
recipient will have to download it. Unless you're using a proxy 
server, this will mean more traffic is generated.

So nice that you are thinking of the users.  Linked attachments are a 
way to dedupe the mail infrastructure.  If my mailserver doesn't have 
to handle multiple copies of a 50 meg attachment then it's a win for 
the infrastructure.  Both outlook and thunderbird either support this 
kind of attachment linking either out of the box or with plugins.  The 
users used to be able to select whether or not to link the 
attachments, why take that feature away?

This was intentional.

Linked attachments are designed to workaround transport and/or storage 
restrictions.  These are admin things.  Users should never be asked 
questions about the technical structure of their e-mail messages, 
especially since they have no control over where this data is stored 
(things might be different if the user could add links to *existing* 
linkable data.   But that's not what linked attachments are designed 
for).

Not to mention that linking is intended to be a last-resort option.   
Nobody should be sending linked messages unless there is a technical 
reason to do so, since you are both making it more difficult for the 
receiving party to correctly view the message, and vastly increasing 
the odds that the receiving party will not be able to view the 
attachment data.

The user should be presented the option whether to have the attachment 
as a link or not.  It used to be this way.