Well I don't always have solid reasons for building something the way I do but I'll try and explain it for you.
-the internal thrusters are standard and small because I wanted to conserve space and larger thrusters have a much longer "no-build" area where the thrust comes out. I'm fairly happy with the standard thrust module but small thrusters have been nerfed so I prob wont use that module anymore.
-the alternating pattern for the side missiles is for increased defense. I think this is one of the main reasons the Hyper Monolith has an advantage over a lot of other ships. When an outer missile module explodes it doesn't damage anything around it and will actually serve as added armor to the inner missile modules. Plus the added defense comes at no extra cost money or space wise, and it makes the ship look a lot cooler I think haha.
-Why not? I just wanted to weaponize the hell out of it, but I did make sure that all the weapons on the Hyper Monolith were long range types. I might try and make one with electro bolts though.
Hope this answers some of your questions, thanks for using my ship so much I'm happy to share designs with the admirals here!