Disguise class. 

History with a focus on the current power centers in their city/region/nation, so they know who their killing or what the implications might be. 

lockpicking

stealth

resist torture

escape from a jail cell

Investigation.

Have a group of seniors stage a fake murder and let the young assassins investigate the crime.

Knowing how a law enforcer / detective might follow the clues and hints they accidentally leave will help them figure out how to avoid detection when they graduate.

I would have a class on recon of a target.  They would learn how to measure distances and record them while not being noticed, how to find the best passageway in and out of a target (both inside and outside), where the loot will be found, spot the guards and observe their rounds, and other stuff.

There would also be a class on structural stuff like how much weight can you put on this rope before it is likely to break?  How much weight can you put on this beam before it will break.  When you walk across the floor, where is the best path to walk without making the boards creek?

There are also strategies for checking to see if someone has passed this way.  This would be useful for the assassin to know how to do and what to look for in case they need to defeat such precautions.  For example, hanging a string just above a door that will be trapped if the door is opened and then closed, allowing someone to check to see if the door had indeed been opened when they were not there.

Of course, lock picking, needle traps, and all other basic thieves skills would be included.