Plasma has generally respected custom icon themes. I imagine that if this change does indeed land within the default Breeze icon set, that it would be possible to run either an older Breeze icon set, or a completely custom icon theme to restore colored icons.
I assume Falcom is making the Switch and PlayStation versions (given they’ve done the Switch and PlayStation versions in-house for Daybreak/Kai and Ys X on the same engine), and either them or GungHo are doing the PC port. At the very least Durante confirmed on Reddit that neither he nor PH3 are involved in the announced PC port (yet?): https://old.reddit.com/r/Falcom/comments/1hhlayv/the_legend_of_heroes_trails_in_the_sky_the_1st/m2st366/