MOD NOTE: For current trinket information, please see the last few pages of the thread. Any discussion at the beginning is highly outdated - both before changes, and before modeling of trinkets was being done accurately. The current newest results can be found HERE (this is a link).
If your question is simply "which trinket is better for assassination" and you're not using RoRO (don't use RoRO), ask shadowcraft.
So, with the RPPM nerfs I was thinking about our trinket choices a bit, and I think that heroic bottle may actually be superior to the normal mode Bad Juju.
A bit of napkin math, using 2.72 as agility EP and 1.15 as mastery EP (stat weights at t14 BiS gear):
Mastery: 1218 mastery - 1400.7 EP
Agility: 3653 agility, 45 second ICD, 20 second duration. Maths out at a maximum of 44% uptime, logs show it averaging 42.5% uptime. - 4222.9 EP
Total: 5623.6 EP.
Mastery: 1467 mastery - 1687.1 EP
Agility: 7333 agility, 20 second duration, 0.5 PPM. Averages out to be 1222.2 agility before "true haste" effects. Factoring in 15% average haste from heroism and gear, this is raised to 1405.5 agility. - 3821.6 EP
Total: 5509.7 EP
Obviously the voodoo gnomes add a small amount of dps and the effect of the trinket is variable on your haste. However, as it stands, Bad Juju is rather terrible for being twenty item levels higher.
TL;DR, you'll likely be using your heroic Bottle until either heroic Bad Juju or until you have tons of haste on your gear. Hooray RPPM nerfs.