>>I've been keeping snakes for two years now, but I've raised them from hatchlings (or in one case a yearling)
Congrats you're doing well! 
>>...they're just now getting bigger...
They will continue to do so - and their needs will change accordingly. They will need more space, larger hides, and larger food items less often - which will mean less frequent, but larger poop.
>>...unanticipated problem...{with the}...liquid part of each snake's bowel movement...newspaper substrate doesn't absorb any of the liquid...
Newspaper is like any other absorbent material, it will only absorb so much, so fast. Larger amounts of liquid will require larger amounts of adsorbent and/or longer times to be absorbed, whether its newspaper, aspen, or what have you.
There are two routes you can take - First is to use more of the absorbent you are already using; Second is to change to something that does the job better, i.e., a better absorbent (see below).
>>I'm worried about bacteria.
Bacteria are always everywhere - don't believe the ad propaganda about "ACME Cleaner kills 99.9 % of germs on contact!" - that's BS. There are literally 10s of millions of bacteria on every square inch of what we would consider clean surfaces! Killing 99.9% of 10,000,000 bacteria leaves 10,000 bacteria behind - the ones that are most resistant to the cleaner!
The point is, no snake lives in a vacuum - there are literally tons of bacteria in the wild, and yet snakes have thrived for 10s of millions of years. However, in captivity, for whatever reason, snakes do fall victim to infections. The solution is reasonable precaution and general cleanliness. Not fanatical sterility.
>>I really feel like I should be changing hides as often as I change paper...I can't imagine where I'm going to get enough boxes...
Cardboard boxes can make acceptable hides. They are cheap and disposable. If you have a ready supply of used boxes you will be fine. One thing to watch out for is what was in the box previously - I would never use a box that contained food prone to spoilage, hazardous materials like pesticides, or that might be hazardous in and of itself. Make sure to throw them out when hopelessly soiled.
>>I'm thinking about...switching back to aspen substrate...
Is aspen better than newspaper? This is an endlessly debated topic. Personally I feel they each have their uses, advantages, and disadvantages.
I like newspaper for hatchlings because there are no splinters, and it can be shredded to make nice fluffy cover. With newspaper, poops always show, so the cage can be cleaned when its needed. However, unless you have a pretty big cage, it can't be spot cleaned. Snakes like to get under newspaper, which means any mess is right on the cage bottom - however, newspaper is easily folded or trimmed to fit almost exactly. Newspaper is abundant and cheap. You can read it twice - once when you get it, and again when it goes in the cage. Its also nice to see some of the folks who show up in the paper get their just desserts!
One safety consideration for newspaper - never ever crumple up or throw away used newspaper until you a absolutely positive the snake isn't hiding in it!
Aspen looks better and can be spot-cleaned, but also can hide poop and other things that should be removed. It may contain wood mites, which are harmless but icky. It can be ingested with food, which can be a serious problem for smaller snakes, but rarely bothers large individuals. Some snakes don't seem to like it and will avoid contact with it. Some keepers have reported apparent allergic reactions, e.g., sneezing, wheezing, by snakes housed on aspen. Its messy to clean - no matter what I do I always wind up having to vacuum the floor after messing with it.
>>...or find hides that are more easily washable...
There are many commercial hides out there, some purpose made ones are quite nice - both functional and decorative. The hollow-bottom dog/cat bowls are useful. The choice is up to you!
Enjoy your snakes! 
John D.
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I am so not lesdysxic!
0.1 Creamsicle Cornsake "Yolanda"
1.0 Bairds Ratsnake "Steely Dan"
0.1 Desert Kingsnake "FATTY"
0.1 Black Rat (WV Rescue) "Roberta"