1) Is there a stacking penalty for navy just like in HOI3?
Sort of. There is a penalty for too many carriers, as previously mentioned, which can be eased by researching higher base control doctrines.
2) Is there a combined arms bonus for land unit just like in HOI3?
Again, sort of. There are two elements similar to HOI3. First there is an element similar to combined arms based on the "hardness" rating of a division build. If that rating is above 40%, it doesn't give a CA bonus of itself, but the division then qualifies for the leader trait bonus of your Panzer Leader generals, e.g. Guderian, Rommel, etc.
Also, like HOI3, when your unit has higher armor than an enemy unit has piercing, you suffer greatly reduced damage while the enemy suffers increased org loss. And vice versa, of course.
3) Does capturing London (by Germany) trigger Soviet Union DoW just like in HOI3?
No more automatic triggers. They have pretty much erased the old event trigger system. In the case of the Soviets, Germany should always have at least a little warning before an attack comes, assuming they took the MR Pact, because the Soviets must first withdraw from the Pact and then either fabricate a war goal or complete the focus tree chain that gives them one. If you watch such messages, you should see it coming in plenty of time to shift your forces back into position. Or, better yet, kick their door in before the thought even occurs to them.