There never was a limit of 1000 marines. Thats just a general guideline for the marines in the main companies. It doesn't include command staff such as the chapter master, captains, the librarians, chaplains, apothecaries, techmarines and tech adepts who're part of the armoury and so on as they aren't strictly part of the fighting body of the chapter.
This. Chapters were never limited to strictly
1000 men. Not only would there be graduating classes of scouts of slightly different sizes (marines in all but power armor, say), but command staff, specialists (tech marines, apothecaries, etc), and advisors of all types. I think that even the most devout warrior would see the pragmatism in having another recruit squad or two, ready if not deployed.
I have always felt that the number "thousand" was to be taken liberally, both in chapters and marines per chapter. If the space marines serve the Imperium so well, then it would take little convincing to get the governing High Lords to permit some leeway in their recruitment. Rate of attrition, and all. Plus, there are chapters who consist of a few thousand, such as Black Templars. In the Badab War, it only became apparent that the Astral Claws were "violating" this limit when they reached four to five thousand...yet they still thought of themselves as loyal.
Even then, I believe the number "thousand" is supposed to be more reflective of the dark age mindset in the 40th millenium. Rather than try to memorize the exact numbers and dispositions of a largely independent fighting force, citizens and soldiers alike would be told, "thousand", because it is easy to envision. Most of the fluff is told as interpretation instead of fact, anyway.
tl;dr - Poetic use of the number "thousand" is not necessarily literal.