I'm yet to face any subCM, but all it can do is damaging my Heatran if it comes in on Forretress (since I'd "waste" a turn placing Spikes, if I'm not expecting that), since after I discover my opp has a SubCM Giratina, I'll start playing the game conservatively, using Forretress to lure out Giratina, bringing its HP down on hazards and possibly kill it with Ho-Oh.
The main problem with Giratina is that it is a sitting duck, also, it'd leave me more Kyogre weak than I already am.
About the Hippowdon issue, if I see Hippowdon and Excadrill on my opponent's team, I'd never let my Groudon getting weakened before Excadrill is severely damaged / out of the game. I can always play around it with Ho-Oh / Groudon (if Rocks aren't up), Arceus can survive an hit and hit back for good damage, Palkia survives an hit and kills it back, I don't find it problematic at all. Also, I've always found winning weather wars pretty easy with this team. Granted, it's not a team easy to use.
I'd provide replays of this if I had any good replay of this team on this comp, if I find any on my other comp, I'll add them on Friday
Luck>Skill—Patron of virtue, Rome's best champion, / Successful in the battles that he fights