Today 3DS firmnware has been updated to V4.0.0-7, which has been confirmed that blocking flashcarts again, but nearly most popular flashcarts are still working on the new 3DS firmware directly or after a firmware update. Here is a list about the working and non working flashcarts.
R4i Gold 3DS (r4ids.cn) with icon
Acekard 2i (HW81) (acekard.com) - Updated for DSi 1.44 before
R4i-SDHC 3DS (r4i-sdhc.com) - Updated for DSi 1.44 before
R4i Gold Plus (r4ids.com) - Updated for DSi 1.44 before
R4iTT Purple / Black (r4itt.net) - Updated for DSi 1.44 before
R4i-Gold Pro (r4i-gold.com)
Supercard DS2 (supercard.sc) - Updated with firmware v1.15 before
R4i-Gold 3DS (r4i-gold.com)
R4i Gold (non-3DS, r4ids.cn)
M3i zero GMP-Z003 (m3adapter.com)
So just remember, don't update your flashcart unless you make sure your flashcart can work on your updated console.