It will be a business decision CBS Home Video will make whether they will pay for visual effects to be rerendered and edited in to a new HD master before the Blu-ray seasons are released. They may feel not enough people will purchase it on Blu-ray to warrant the additional costs.
While you may be right, I am still dubious of your claim. Can you post something more recent than the March 2002 article you posted in TNG forum? Since that date UPN started broadcasting ENT in HD and the entire series has been sold to the HDNet channel. If the visual effects of any first season episode was done at lower resolution then it may have been upgraded already, and I haven't seen anything to indicate that the latter seasons were done at lower resolution.