Did you forget to install libctru?

I have latest development tools installed with dkp-pacman

It's definitely not using the right gcc, that's the system version. What's the output of which arm-none-eabi-gcc? And if it's /usr/bin/arm-none-eabi-gcc, what's the value of $PATH?

demetris@demetris-TA770E3:~$ sudo dkp-pacman -S 3ds-dev
:: There are 13 members in group 3ds-dev:
:: Repository dkp-libs

1. 3ds-examples 2) citro2d 3) citro3d 4) devkitarm-crtls 5) devkitarm-rules 6) libctru
   :: Repository dkp-linux
2. 3dslink 8) 3dstools 9) devkit-env 10) devkitARM 11) general-tools 12) picasso 13) tex3ds

Enter a selection (default=all):
warning: 3ds-examples-20200417-2 is up to date -- reinstalling
warning: citro2d-1.3.0-1 is up to date -- reinstalling
warning: citro3d-1.6.0-1 is up to date -- reinstalling
warning: devkitarm-crtls-1.0.3-1 is up to date -- reinstalling
warning: devkitarm-rules-1.0.0-1 is up to date -- reinstalling
warning: libctru-1.8.0-1 is up to date -- reinstalling
warning: 3dslink-0.5.2-2 is up to date -- reinstalling
warning: 3dstools-1.1.4-2 is up to date -- reinstalling
warning: devkit-env-1.0.1-2 is up to date -- reinstalling
warning: devkitARM-r54-3 is up to date -- reinstalling
warning: general-tools-1.0.3-1 is up to date -- reinstalling
warning: picasso-2.7.0-1 is up to date -- reinstalling
warning: tex3ds-2.0.1-2 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (13) 3ds-examples-20200417-2 3dslink-0.5.2-2 3dstools-1.1.4-2 citro2d-1.3.0-1 citro3d-1.6.0-1 devkit-env-1.0.1-2 devkitARM-r54-3 devkitarm-crtls-1.0.3-1
devkitarm-rules-1.0.0-1 general-tools-1.0.3-1 libctru-1.8.0-1 picasso-2.7.0-1 tex3ds-2.0.1-2

Total Installed Size: 298,88 MiB
Net Upgrade Size: 0,00 MiB

:: Proceed with installation? [Y/n]

demetris@demetris-TA770E3:~$ which arm-none-eabi-gcc
/usr/bin/arm-none-eabi-gcc

And the value of $PATH?

demetris@demetris-TA770E3:~$ printf "%s\n" $PATH
/home/demetris/.local/bin:/opt/devkitpro/tools/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

I'm assuming the answer is yes, but does /opt/devkitpro/devkitARM/bin/arm-none-eabi-gcc exist? This may be an issue with how I have CMake searching for paths. CMake can be really opaque sometimes.

demetris@demetris-TA770E3:~$ ls /opt/devkitpro/devkitARM/bin/

arm-none-eabi-ar         arm-none-eabi-elfedit     arm-none-eabi-gcc-nm      arm-none-eabi-gdb            arm-none-eabi-lto-dump  arm-none-eabi-readelf
arm-none-eabi-as         arm-none-eabi-g++         arm-none-eabi-gcc-ranlib  arm-none-eabi-gdb-add-index  arm-none-eabi-nm        arm-none-eabi-run
arm-none-eabi-c++        arm-none-eabi-gcc         arm-none-eabi-gcov        arm-none-eabi-gprof          arm-none-eabi-objcopy   arm-none-eabi-size
arm-none-eabi-c++filt    arm-none-eabi-gcc-10.1.0  arm-none-eabi-gcov-dump   arm-none-eabi-ld             arm-none-eabi-objdump   arm-none-eabi-strings

http://dpaste.com/1M95HKR

You can use triple-backticks around lines to make them code blocks.

Anyway, I've managed to reproduce the issue on my end and will look into it further.

good news, thanks

You will need to delete your CMakeCache.txt before you can try again

now it complains about this:
[ 96%] Linking C executable mgba.elf
[ 96%] Built target mgba.elf
Scanning dependencies of target mgba.3dsx
[ 97%] Generating mgba.xml
[ 97%] Generating mgba.smdh
/bin/sh: 1: BANNERTOOL-NOTFOUND: not found
3ds/CMakeFiles/mgba.3dsx.dir/build.make:66: recipe for target '3ds/mgba.smdh' failed
make[2]: *** [3ds/mgba.smdh] Error 127
CMakeFiles/Makefile2:718: recipe for target '3ds/CMakeFiles/mgba.3dsx.dir/all' failed
make[1]: *** [3ds/CMakeFiles/mgba.3dsx.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

You need to install bannertool. You should also install makerom from Project_CTR so the cia builds.