I think this forum is safe now...I hope anyways! If not I'll have to disappear again.
Saddle bags can be small and lightweight or large and heavy, to get a saddle bag that can handle a mini pump that can actually pump a tire up to 100 psi has to be on the longer side of the pumps so it has enough volume with fewer strokes and less effort, so you'll need a larger bag, which I think is not the idea situation when a mini pump comes with a mounting system that can attach to your bottle cage mounts and will mount the pump to the side of the cage, nice and convenient. There's only about a half a dozen pumps that will actually reach 100 psi, the rest won't even though they say they will, and some might but with a huge number of strokes and a herculean effort.
Some bags come with straps underneath the bag on the outside but I've found those straps to slowly stretch over time then one day you hit a bump and off flies your pump!
There are a lot of good saddle bags that can work for all the needs you listed except to carry the pump inside. I happen to like Topeak Aero Wedge, the come in small, medium and large, I like the large size when I'm riding far like touring, but if you don't need that much space go with the medium. I can put in the large my spare tube, tire irons, a Park MTB3 mini tool, folding pliers, several little packets of hand cleaner, fire starter stuff (remember this is for my touring bike) and some other stuff I can't recall right now, all that stuff goes into a plastic zip lock bag so as not to get wet, an Altoids tin I designed so I can carry all my small stuff in including money and patches just to name a couple.
I did find another bag that I also am trying out to see if it will last like the Topeak does, the Topeak's are very well made and can last 10 years or longer, but this bag is called the BV Bicycle Strap On bike saddle bag, it's sold on Amazon for $12 for the large, it's made of the exact same materials as the Topeak, and it also expands but only out the bottom instead of the back so the bag doesn't get longer. The BV large size is about the same size as the Topeak Aero Wedge medium. Most of the time when I know I'll be out after dark, I take my cell phone bar holder off and put the cell phone in the bag and a headlight on the bar, and if I need to I will expand the bottom of the bag to accommodate the phone, but I carry all the basics like a tube, tire irons, older Park MTB 2.3 (I think that was the number), several packs of hand cleaner, and the Altoids tin I use when I tour. For the price the BV bag seems like a great deal, I've had it for 2 years and no signs of wear yet.
No saddle bag have I've ever used is waterproof, so I do spray my saddle bags, (and my handlebar bag I use for touring which is another Topeak bag), with Kiwi Camp Dry heavy duty water repellent spray, I give them two coats every season. When I tour I take the extra precaution of putting all my stuff in ziplock bags because I probably won't have a choice but to ride in rain and sometimes it can be intense rain, even all the stuff in the handlebar bag is all in ziplock bags. I also use a black crayon and rub the zippers with it, this sort of gives the zipper some water seepage protection but it also makes the zipper work easier.
