I just heard about and installed Lakka yesterday. It took me awhile to solve this problem, but it is actually very easy.
So the guide linked above is for Glupen64, which I guess is an ARM version of Mupen64. Once I realized that, it’s obvious the above instructions can be used for Mupen64.
Start up a game in Mupen64. It will then create a Mupen64 folder in your “System” folder. Inside that folder, create a new folder called “cache”. Inside the cache folder, place the HTC file (make sure it follows the file naming format exampled in the link above. I.E “THE LEGEND OF ZELDA_HIRESTEXTURES.htc”.
In the Muppen64 core settings be sure to turn on the Hi-Res textures option and switch the plugin to Glide64. After that, be sure to restart the retroarch service and Mupen64 core and then load up your game. The texture packs should now be integrated into the game (make sure you turn on all the other post-processing goodies that the emulator offers too).