Late My Number card renewal?

Yes, I know I should not be late but I will go in to my local City Hall to apply for a new My Number card and the staff told me that it will cost me 1,000yen. That is no problem. I currently have permanent residence status and I have had it for a couple years now. I do not need to renew my PR for a few years from now. I am wondering if record of my late My Number renewal/new card registration will have a direct negative effect when I go to renew my PR status?

Nope - no impact at all. My card expired ages ago, but the number remains valid. Renewal needed to be done before it expired, and due to unfortunate timing I missed by six days. To get it re-issued will be a PITA and the people I spoke to at city hall about it said don't bother (because it is actually quite a complex process - I've done that before too).
In related news, I saw the uptake of the MyNumber system has managed to climb to 25% nationally - it is not that wide spread, most people simply don't need it.

Thank you for your message and sorry for my late reply. I actually did find out that it is no issue at city hall. I will go there tomorrow and apply for a new card and I just need to pay like 1,000yen.