Did you just happen to miss the theming in the snake and booby trap tunnels. The volcano one I can understand because those lights burn out quickly and take some time to replace.
Ive ridden AE many many times (atleast 3 times each visit) and i have never noticed any theming besides.. The stone arches, the last tunnel, on the first chain lift there are the masks, and a red lightbulb in the first tunnel.
Next time you ride, take a good look at one of the tunnels on each of your usual 3 rides.
The snake tunnel has snakes hanging from the walls and ceilings. They used to have an audio of hissing as you went through that tunnel, but it is so brief you hardly noticed. When it first opened there was a bell that rang on the outside of the tunnel next to a sign that read "Bridge Out" or something along those lines. Which fits into the audio theming in the station if you listen "Track 2 is no longer in use and has been abandoned," "...avoid the deep jungle route as it is now impassable" (Not sure if they still play the voice over the Indiana Jones theme).
The second tunnel (booby trap) there are spears that shoot out of the walls as you go by. Unfortunately, they never got the timing down so either the spears are already out when the train rounds the turn, or they shoot out once you start up the lift so you miss them all together.
Cool! I never knew. I remember some of the effects from the 90s but not everything. I miss the well done theming. It really added to the ride.