I would never associate treats with work. If you do that, soon enough you'll have a horse who always tries to rob your pockets looking for treats and you won't have the attention needed to get the job done.
I think associating treats(or whatever positive reinforcement) with work is actually very important to me. I want my horses to enjoy my company, to enjoy doing what I ask, so they actually see it as play, not 'work'. Creating a strong association with Good Things is a great way to form a good 'work ethic'.
As for horses learning to mug you for treats(or rub on you, if you reinforce with a face rub for eg), being pushy or mouthy, that's about what you're reinforcing
, not what you use to reinforce. I find treat training a great way to 'retrain' bad manners and aggressive behaviour too. My horses definitely associate me with Good Stuff - often food treats - but I've also taught them to mind their manners & they know the quickest way to turn a Good Thing to Bad is to be rude.
To OP, regarding reinforcing specific behaviours, horses live in the present & need *instant* reinforcement *when* they perform a desired behaviour. Giving a treat at the end of a session is just that - a treat. If you wish to use it to reinforce a behaviour, you need to do it in the same manner you would use negative reinforcement(removal of pressure) or punishment - at the time of the behaviour you're wanting to affect.
You can learn more about the principles of training/learning by looking up 'clicker training'. It's basic behavioural psychology, of which the tools - clicker, treats, whatever - are optional. It's the principles that are important to understand.