This has also happened to me (now fixed with re-importing the Master Data) and it was the alert_post_tag that was missing .
Comparing my list of add-ons to those of the OP, the ones we have in common are (some with different version numbers):
******* - Change Threads/Posts Owner 1.0.4
Last Post Avatar by Waindigo 1.1.8b
Nodes As Tabs 1.2.2
[8wayRun.Com] XenPorta (Portal) 1.6.0
[bd] Tag Me 2.0.1
I think the blank alerts have only happened recently though, which I guess would rule out many of these as they have not been changed for a few weeks. The only exception to that is Nodes As Tabs which was updated at the end of September. Looking back in my emails, I received an email about a tag in a post just before updating Nodes As Tabs and I'm sure I'd have spotted a blank alert then.
Could Nodes As Tabs have anything to do with this? I'd have thought not, I don't think it has anything to do with the alert_post_tag template?
The only other possibility that I can think of (and would be more likely) is Tapatalk, which I uninstalled on 17th October. Now I know that it uses alerts and searching the install XML file I found
Code:
<template title="alert_post_tag" version_id="8" version_string="1.1.4"><![CDATA[{xen:phrase x_taged_you_in_post_in_thread_y,
'name={xen:helper username, $user, 'subject'}',
'title=<a href="{xen:link posts, $content}" class="PopupItemLink">{xen:helper threadPrefix, $content}{$content.title}</a>'}]]></template>
</templates>
(and yes, they have misspelled the phrase!)
Could it be uninstalling Tapatalk that has removed the alert_post_tag template? The above is the only reference I can find to the template in Tapatalk, I can't see a reference to removing a template unless I should be looking for something less obvious?