OP, you're pregnant and probably feelings things a bit more emotionally than you normally would, and all the more-so because you don't really like your boy being in nursery anyway. You cant see the woods for the tree's
I think I would go down the 'let's clear this situation up once and for all' route and I would have a meeting with the head of the nursery to discuss my sons progress or otherwise, as well as address any other concerns they may have about him.
No-one in a nursery setting should be able to tell a parent a child needs assessed unless its done in the proper manner, so bring it up at the meeting and say - X suggested he be assessed and I was wondering why she thinks its necessary, if its something we should be considering, and if he does need assessed why is it left to an assistant to tell us? Let the nursery people then sort it out and if your son does need an assessment at least it gets the ball rolling, and if he doesn't then you'll know it cant be used as a throwaway line ever again if he has a bad day. And not just because they'll probably be told - its not your place to say this to parents so don't do it again.
The kicking under the table - I think you would have been mortified anyway you were told but just as you have to take on board that he did it, the nursery also need to understand that there are ways to pass on news and there are ways not to. And to say a child is sneaky isn't a good way to go about things.
Your husband getting him late to bed - that has to be worked on.
No routine in the morning - again you have to sort that out.
Also, be honest with the staff as to the way you're feeling about your boy being in nursery because I suspect that no matter what nursery he went to you'd be feeling fragile about it right now. I also think its possible the assistant doesn't like your wee boy and is letting her dislike of him show when she mentions things to you, and perhaps him. Where did the 'bad' come from? So a meeting where you all end up on the same page re your son, what nursery expect of hi, what you expect from the nursery, will be a warning shot over her head and her attitude will have to change. Everything will be out in the open and there can be no excuse for anything else she says or does in a less than professional manner.
I think we have to get over the idea that all nursery staff are saints just as we have to accept as parents that sometimes our wee ones can do things that mean we are put in a position where we are left feeling very uncomfortable and with lots of thinking to do.