Hi,
In my save i have set water to 0.25 speed and deep water to 0.1 speed, but the biters are not affected at all by it. they can run at full speed across both water types

This is kind of by design or by virtue of the limitations within Factorio. I think it is fitting that the natives know very well how to navigate their own environment.

The biggest issue is that biters don't respond to tile speeds like players do. If they did this would be very taxing on the pathfinding as it would need to read the speeds for each tile. Considering that path finding can already lag your game quite a bit this would only make it worse. Another approach I could think of is adding "stickers" to biters using scripts when they pass over tiles but this is also very laggy since doing this from script on every single biter (possibly thousands) is very much not optimal. So I've opted to not "fix" this although I'm also of the mind that this does not need "fixing".

If a solution to controlling bug speeds on a per-tile-type basis is ever reasonably available, I agree biters shouldn't swim at 44-65 km/h.

Yes, the bugs are native to the planet, but they are not fish. Physiologically, they aren't adapted to swim and exclusively inhabit terra firma. Thus, biters would also be slowed down by water, but not as significantly as the character is - notionally, 65%/50% speed coefficient over the 35%/25% of the character. And maybe furthermore, having a lesser shallow water penalty as the size of the bug grows. A behemoth biter would probably be able to touch the floor in the water, its legs shaped such that it could grip the floor well enough to overcome hydrodynamic drag for a decreased movement penalty; whereas a small biter would practically be bobbing even in shallow water. That might reflect the bugs' ability to adapt to their environment, too - at least as much as they can without growing fins.
I also think it's logical for water to be an obstacle for the bugs, just not an insurmountable one as it is in vanilla, and one easier to overcome as evolution factor increases. When allowed to move across it at full speed as they would open terrain, that is not the case.

Hopefully a viable solution to the technical problem will present itself someday.