Strategic bombers suffered heavy losses in WWII, so I hope they will in this game, too, especially if the people you're bombing put lots of industry into AA and planes. It should be a real strategic consideration, especially for countries like Italy and Britain which aren't superpowers: you can build a powerful bomber force and give it lots of fighters and try to wreak havoc on enemy industry, but if you do, you'll have significantly less industry to spend on land forces, your navy, and so on.
Both of which cost industrial power. It's the same system, basically, just that in HOI3 it's abstracted into "strength" and "reinforcements", whereas in HOI4, you build and track actual planes, guns, tanks, etc. Without knowing the actual numbers, it's impossible to say if bombing is more risky in HOI3 than in HOI4. We never even had a concrete idea of how many planes constituted a "wing".
As you say yourself, in HOI3 you needed to put IC into reinforcements (and every IC point spent rebuilding losses was an IC point not spent on supplies, consumer goods, lend-lease or building or upgrading units) -- likewise, in HOI4, you need to put industry into building planes. Losing planes may have the same impact in HOI4 as in 3, or a lesser impact, or a greater impact. We just don't know yet.