What's the lore explanation for April losing her tan and freckles? Is Daisuke just evil?
Short answer: There isn't one. Simple design change.
Slightly longer answer: Daisuke Ishiwatari isn't the only character designer for Guilty Gear and it may not have been his choice. Looking at art we know for sure he's drawn and colored, he's generally very good at giving characters varying complexions and physical features, which often don't make it into the games. This piece from Artworks of Guilty Gear X 2000-2007 is a good example. Not a single character here has the same skintone.
In Character Designer magazine, issue 1 (fall 2003), Daisuke mentions Justice having been designed by another (unnamed) member of the team. It also implies more team members helping with character designs around the start of the Guilty Gear XX series too, and that management above Daisuke often stepped in to make design changes he didn't always agree with. Junya C. Motomura worked alongside Daisuke for Overture and, for Xrd and Strive, art direction has been handled by Hidehiko Sakamura. Also with Strive, Kenta Asano has been handling a lot of the merchandise and collaboration illustrations too — not Daisuke, as in past games. Though Asano is pretty good at not whitewashing characters or drawing them off-model (he did the Tower Records and 0101 collab art).*
Guilty Gear as a series is usually pretty good at being respectful with things like skin color, but it's not perfect and it wouldn't be the first time they made an odd change like this. We won't know if this change for April was Daisuke's decision or not unless it's brought up in an interview somewhere. Evidence suggests it may not have been, however.
*Tower Records: Vol.1, Vol.2; 0101: 2023, 25th Anniversary
