Short Answer: Yes, the traits (not features) should change as they are inherited from the Creature Type. "Special Qualities" would apply to anything the base creature has that isn't a part of the creature type, such as breath attacks or spellcasting ability.
Long Answer: Here's the way I would do it:
1) and 2) As the half-dragon template changes creature type to Dragon, you look up that creature type and apply the relevant traits (but not features). As this has replaced the creature type Vermin, you ought to be removing any traits gained from that (unless they were also in Dragon) - however, see 4).
3) If something applied in the template invalidates a previous trait, such as +2 intelligence taking it over the limit for mindless, then remove the trait. In this particular case though, the creature has stopped being Vermin and is instead Dragon and therefore loses that trait anyway. If you really wanted a mindless half-dragon vermin, see 4).
4) Optionally, use common sense to tweak if doing any of the above results in it feeling wrong. If in your game's universe you feel a specific half-dragon creature should not have certain dragon traits, remove them. If something was changed to be partially something else via a template, you may want to keep some or all of the traits that any change in Creature Type has removed. For example, you may want your half-Dragon-Vermin to still be Mindless to represent having physical dragon features with a vermin mind (in which case you could add that trait back in and remove the +2 to intelligence).
For clarifications, see http://www.d20srd.org/srd/improvingMonsters.htm#templates (thanks @Tridus !)
