Cut the subfloor to slide it in around the pipes.

I would assume this will be flooring under a cabinet. If so, pretty isn't important, a level surface for the cabinet is. Use a round drill bit to make the holes and a jigsaw to continue the holes to the wall.

You can do as others suggested but I would use this as an opportunity to clean up and modernize your piping. Those valves are a potential for another leak to ruin your new work. Are you in a cold climate where you can't put the pipes in what I assume is an exterior wall? Always nicer to have pipes come out of wall.

I prefer to have pipes not in exterior walls, even in warm climates I've seen a freeze cause lots of water damage.

There are all kinds of variables here. Is this above a crawlspace? A basement? Can you get under there to work from below? What kind of flooring are you putting back down? Is your current subfloor in good enough shape that it doesn't need any structural help from whatever you are putting over it?

At the very LEAST I'd cut the copper right below those shutoff valves and put new modern shutoff valves and supply lines to the sink and dishwasher. I'd never recommend enclosing a "push-to-connect" coupling in a wall even though you technically can now by code(I just don't trust them that much), but you wouldn't have much trouble just pushing a couple Sharkbite valves on the cutoff copper that are already threaded for your supply lines. You'll have to get a "T" and shutoff for your dishwasher hookup I see there as well.

Also I see you have a big old copper drain line there which tells me almost certainly you don't have proper venting based purely on the age of the home. If you don't want to tear open walls and do attic work to vent to the roof, you can put a loop vent in like they do on a kitchen island(assuming you have at least one location in the house to tie to) Don't miss this opportunity while you have everything apart. You want your kitchen sink vented for sure.

Plumbing isn't super hard but it is super hard to get all the details right. If this all sounds complicated I'd maybe get a plumber in to rough everything in for you.

I agree with cleaning up the piping and new shut offs. Have plumber come and cap the plumbing. Then you can drill holes to fit over pipes. After all the flooring work is done (and sink cabinet installed with just 2 or 3 drilled holes (where is the drain line?)). Neat and tidy. Makes things easier.

I am in a mixed climate (Michigan).

This is the floor above a heated basement.

This will be under a base kitchen cabinet holding a sink, so pretty isn't as important, I rather err on the side of safety and reliability first.

I will be putting down a floating hardwood floor (waterproof most likely).

Current subfloor seems alright, but also I am not an expert. Ideally I'd replace the bottom layer, it appears to fray a bit at the end, but also maybe I can clean it up and seal it instead (?).

The copper drain line is vented to the roof - there is a pipe sticking out of the roof that seems like the vent pipe.

Well okay so plumbing stuff aside how thick was the layer of plywood you took out? 1/4"? 1/2"? Are you putting granite or heavy stone in on the countertops?

layer of plywood I took out was 19/32"

Okay so 5/8 essentially. If you are putting granite in, you want at least that thick back on top, if not 3/4". If the feet of your cabinets fall in a joist cavity in front or back, you don't want deflection when the granite goes in. Shoot for at least 1.5" of solid wood in the joist spans. The second sheet would be screwed 6" on center in the field and 4" at the edges with deck screws that penetrate fully through both layers.

If you don't want the floor to raise that much, the other option would be put 1/2" 4-layer span rated AB underlayment rated plywood in, and then go up under the floor and put 2x4 blocking in where your cabinet feet will fall.

Capping the pipes will also make installing the cabinet easier as you can drill the holes in the base and drop the cabinet over the pipes. And then use an escutcheon to cover the holes.

OK...I'm going to address the Elephant in the room. Have you investigated the black mould-looking stuff that is making some of the remaining wood look nasty?

And yes...the bottom layer of plywood is looking pretty tatty. There are old stains, it is flaking, there's black mouldy looking stuff in the batting and on the wood and on the framing. And I *think I see some rodent droppings in the second photo of the subfloor (second to last photo).

All of these are indications that there is a LOT more going on there than just wonky pipes. If you do anything, please get the right professional to do it. For pipes we use a Certified Plumber. For electrical (I see some old wiring leading up to that junction box) please use a Certified Electrician. For mould removal (in small areas) use an N95 mask, safety goggles and a STRONG bleach solution ('cause Hantavirus is not a nice thing to have to deal with if those are mouse droppings).

I know you want to hurry up and get your floor in, but you have an IDEAL chance to FIX what is wrong with this set up. Like I said there are more issues than getting subfloor around the pipes (which look old and have been repaired MANY times...count the number of 'green' stains you find on each pipe...each stain = corrosion = repaired in the past).

Bleach is not the best product for mold. Concrobium is a much better product.

Bleach is for animal feces and dried urine.