If I am using a bolter with special ammo should I use the regular X critical charts for a critical hit or use ones that seem more appropriate? For instance I get a critical hit with a hellfire or dragonfire round I was thinking that maybe E crits would be more fitting. If I get a critical from a metalstorm round would rending be the right critical table? For implosion shells.... I have no idea what the right critical table to use would be. I think stalker sounds would use the I critical table.

Has this been ruled on before?

By RAW you change critical table only if special ammo change damage type. In Deathwatch distinctive features of special ammo are in additional rules, not damage type change.

I would say that some ammo are Energy instead of Explosive. However, first it's not said anywhere in a rules so you would need to house-rule it, and second, Explosive weapons are more effective against Hordes, so it would weaken them in this way.
Of course, some Energy Criticals are better than Explosive (for example, Energy 6 on Head kills, and it's only Critical to kill on 6), and their effects are different, so theoretically you could argue than one is superior to another. However, I'd just say that you should do as you want, either way it should not have that much impact on gameplay and if you're using mainly Bolters it will make a nice change to hear about their face melting instead of ripping off sometimes ;).

Again I read that some special ammo replaces the exploding warhead with incendiary elements, so I assume they would do fire damage and flamer critical are E.

Hellfire uses acid which I suppose produced damage sort of comparable to fire so maybe E crits are good for it too. (Say, if I use hellfire ammo on a horde of tyranids should it get a bonus since hellfire was designed to fight them and it ignore their armor? )

Metalstorm rounds use shrapnel like a frag grenade so rending seems right as the explosion doesn't do the damage, the shrapnel does.

Stalker rounds replace the explosive with a 'solidified mercury ' slug so i'd think it wouldn't do E crits but I crits.

Again that implosion round... I have no idea.

I may house rule this if I can do a good critical for implosion rounds. We did have a scenario where the KT was ordered to find and capture the mist reaper and naturally took some implosion rounds. (GM discretion: I let the base commander fail a 'save vs. Common sense' roll and issue all bolters a 'free' clip of implosion shells since they were the stunningly obvious best choice to capture a live one with.)

The players made their own failed save vs. Common sense (it seems like most forces in the imperium have an automatic resistance roll to avoid common sense.) and made called shots at the legs which I allowed to do extra mobility damage on successful hits. After slowing it down while minimizing the risk of killing it a couple more shots were aimed at the scythe arms to impair them and, well, the arch biologos at fortress Erioch got a nice new pet to play with. (The arch biologist was last heard overseeing the transfer of the mist reaper to the labs while saying ''I will feed him and pet him and call him George! '')