Deer mice carry a lot of diseases that can infect your mice (or you, for that matter). From bacteria and viruses to more interesting internal and external parasites, there's a lot that's transmissible between deer mice and house mice. There are also a few diseases we can catch from them. Use gloves. If you have an air filtration mask, like used when mowing lawns, it helps to wear one while cleaning out their cage. I would not allow the house mice to share airspace while you keep the deer mice, to reduce the risk to your pets.
Also, from experience rehabbing deer mice, I can tell you that they don't calm down, no matter how young you get them. Tame deer mice are that way after many generations of breeding for calmer mice, and that's assuming they don't up and have a heart attack on you (very common) before you get there. Their diet is a little different from our mice, and they tend to be difficult to keep alive once they've been doing poorly. At two weeks of age, her pups don't have long at all until they'll be weaned. I'd release them once they're weaned, were I you. If you do decide to keep them on, you'll want to start a bug colony of some variety. They go through a lot of insectoid protein, and farming mealies, crickets, or roaches will be the most effective way for you to keep ahead.
