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Instead of Roboute Guilliman going all the way in dismantling the Legions and their supporting assets like Imperial Navy and Army, he makes Codex Astartes rules like this:

Each Legion is dismantled into HH Chapter size of 10000 Marines.

All Imperial Navy and Army Ground forces under a Legions' command are evenly distributed to the newly found chapters.

The Chapter Masters are in command of all the forces.

How does this affect the coming ten thousand + years?

For the worse.

The Chapters would rarely have a noticeable increase to their operating size per engagement (1000 Marine Chapters still deploy proportionally to the conflict they're in, having more Marines would just mean the Chapter takes on more conflicts, not that they would send more Marines to existing ones). Exceptions might occur in places where the Chapter sends all their forces to one location (Salamanders with Armageddon, Ultramarines with the Tyrannic Wars, Blood Angels with Baal, White Scars with the Red Corsair assault on Chogoris), but even then, would the Chapter recall ALL it's troops, and leave countless worlds undefended?

The Ultramarines would gain further ascendancy in numbers, as they were already operating on a very successful recruit and reinforce system pre-Heresy, making them the most numerous Legion. Speaking of, you mention how each Legion would be dismantled into 10000 Marines - many Legions post-Heresy didn't even have that many Marines left, so their galactic influence would have been drastically reduced. Legions like the Iron Hands, Salamanders, Raven Guard, and Space Wolves after Yarant were not in a good shape. Basically, Ultramarines would have gained a lot more political dominance than in the existing timeline.

However, this ignores that this new Codex would probably be a net worse outcome. The risks of a corrupt individual like Huron taking control and causing the ENTIRE group to fall would be so much worse, with an order of magnitude more Marines, and now with human and naval assets. Yes, perhaps there might be more co-ordination in combined assaults, perhaps a degree of miscommunication might be avoided, but the Chapters would still likely be spread thinly (with less incentive to form alliances with other Chapters, hurting inter-Imperial communications that way), and the outcomes of single Chapters being turned to Chaos would have far greater effects.
Imagine something like the Blood Ravens incident, or the Astral Claws, or the Brazen Drakes, happening on a tenfold scale.

TL;DR, minimal benefits, drastically worsened consequences of corruption.

Ok.

How about then if the Marine count stays thousand but they stilm get Guard and Navy units? Or just the Navy unit?

And alternatively, 10000 Marine chapters with no Guard or Navy units.

 Tyzarion_Kronius wrote:
Ok.

How about then if the Marine count stays thousand but they stilm get Guard and Navy units? Or just the Navy unit?

Still providing renegades with more troops, and now, more importantly, ships.

Human soldiers are still deployed alongside Astartes even in current 40k, and they usually give over operational control to Space Marines when it happens. Nothing really changes operationally, except now Space Marines have absolute authority over the Guardsmen, which I don't see ending well.

And alternatively, 10000 Marine chapters with no Guard or Navy units.

Again, very little changes. The Chapters would still be spread out to deal with multiple warfronts, would still engage in roughly the same sized battles, and would grow increasingly insular given that situations where they might call for allies, they will call for their own brethren. Ultramarines would still have the largest amount of successors and actually be large from the beginning, with Istvaan Chapters not even able to form successors due to not even having 10,000 Marines for their own Chapter. And you still end up with too much centralisation of power in the hands of one person. In current 40k, you need 10 Hurons to make an army that big turn traitor. In these proposals, it only takes one.

In the specific example of Huron, it might have prevented the Badab war in that his big grievance was the Imperium never giving him the resources he needed. If he'd had 10,000 marines to call on, he'd have had a shot at actually specifying the maelstrom zone and keeping it pacified.

The problem would instead have been seen wherever the other 6,000 astartes were that in this history are now astral claws, because Huron wouldn't have dispersed them from the maelstrom warders territories.

The consequences of splitting then up into 1000 was made under the assumption that they'd all act independently. But the truth is they act in concert more often than not.

I don't think it would change a huge amount, there wouldn't be any more marines then there is now, they'd just be arranged differently.

Instead of the sons of dorn bring separate chapters that all work together, they'd be a single larger chapter that all works together...