The current legal position in Scotland seems to require obtaining the permission from a 'web site' before you can link to it from your own web pages. Since the Shetland Times case only offered an interim injunction, merely stating that there was an arguable case, it would be wrong to draw too many conclusions. For the time being, as long as what you are copying is for your own private use, I think it is safe to continue to bookmark. Offering bookmark lists is no different from offering bibliographic citations. URLs are facts and there is never copyright in facts, so go ahead and offer such lists to students.
Email is unsafe as a means of doing legal business.
The idea that if you don't receive a reply in 14 days there is no objection is totally invalid in law and should never be used. Failure to reply implies refusal, not consent. Yes, potentially there are differences, but in most country's laws it would not be considered infringement of copyright to provide an active link. It may be considered an infringement of Moral Rights if the link is between two sites that one of the site owners considers impugns that owner's reputation. Generally, though, installing active links should be safe.