It's really up to you which build to go for. I went Affliction and Dark Pact is awesome. It actually increases my DPS since I don't have to worry about my mana as much. I cast Shadow Bolts whenever Nightfall procs or sometimes even when it doesn't. I rarely have downtime and mobs still go down quickly. I respeced at 40 in order to get Dark Pact and haven't regretted it. It's worth giving a try and if you don't like it you can always respec to something else.
I don't know a whole lot about Destruction since I didn't go that route so I can't really give you pros and cons about that build. My build is 32 in affliction, 5 in demonology for Demonic Embrace, and the last 14 in Destruction for Shadowburn and Devastation.
From what I hear Destruction is the way to go for high level instances since there's a debuff limit (i.e. you wouldn't be able to stack on all of your DoTs) but if you're only 40 then it really doesn't matter and hopefully they'll have that problem fixed by the time you hit the high 50's.
As far as Aftermath and CoE stacking I'm not sure but it shouldn't be a big deal if they don't. CoE has a 12 sec duration so you'd have to recast soon anyway. If you go affliction be sure to get Fel Concentration in order to drain tank and Nightfall because instant cast Shadow Bolts are always nice.