Your husband grew up on a farm. I assume they had chickens. Does his experience count for anything?
I don't know what the coop or the rest of your property looks like. A coop that size is not what you typically see in a small back yard. I don't know how dry that coop is or how much poop might be in the hay. I don't know how much room they are going to have outside the coop or how you will manage them, free ranging them or keeping them enclosed in a coop. I assume you are mainly talking about raking the hay out and replacing it with something fresh. It's kind of hard to talk about specific repercussions without more details but I'll try to hit a few possible high points.
The first concern is parasites or diseases that might be in the hay. After seven months with no chickens it is extremely unlikely there is anything in that hay that will harm them that is not also in your soil and the surrounding area. I don't see raking that hay out improving anything in that regard. If you rake it out, what do you do with it? If it did pose a biosecurity threat, it still does unless you totally get rid of it by burning or hauling it away.
If that hay has a fair amount of poop in it, it could be great on a garden or in a compost pile. One standard way to put that on a garden is to clean the coop out in the fall and spread it so by spring planting it has broken down. Otherwise it is probably best to compost it before using it. I don't know what your husband plans.
If there is a lot or dry poop in it then it could be very dusty when they scratch in it. If it is dusty that could be a reason to take it out.
Do you know anything about the history of those chickens that were there? Were they diseased or did they have parasites? If so, which disease or parasite? If you know of any history you need to do a lot more than just rake the hay out.
I'm having trouble coming up with any real practical downsides to not raking the hay out as long as it is dry except maybe the dust. If it is wet, your issue is not the hay, it's keeping that coop dry.