Why can't you use bombs, DDDs, and cynos in high-sec?
Because CONCORD can lock down your modules, and the Empires have cynojammers in their systems.
The "artificial" limitations are already in place, as far as I can see. I'm not convinced that the problems with incorporating it into lore and gameplay (gameplay is already there, imo) are so great. The "drones did it" solution also raises questions.
If you use teleporters to extract loot from cans, why can't you extract your opponent's pod from their ship?
Why can't I teleport a nuclear charge on board my enemy's ship?
Why can't I teleport soldiers aboard my opponent's ship to capture it rather than destroy it?
And that's just the basest level of gameplay questions that would arise. If you have matter-to-energy teleportation you also give rise to these issues:
Why do I need to haul all my stuff across the universe? If mass can be accurately patterned as energy, why can't I convert my entire hangar into a battery?
Why do I need to grind asteroids to bits? Wouldn't it be easier to just use teleporter technology to extract the minerals straight from the rock? Or convert the whole rock to energy and not need to worry about storage space?
Why do I have to travel anywhere? If my character or ship can be converted to an energy pattern, why not just send that pattern via the fluid router system to instantly get materialized where I want to go?
Why do I need to be concerned about losing my stuff? If my ship and modules can be expressed as energy patterns, all I need is a station with a replicator to recreate it all.
Why do I need to build anything? If everything on the market can be abstracted to an energy pattern, why would anyone need to buy something from anyone else?
Yes, you might say "But H! You're super cool and all, but you're assuming Star Trek-type transporters. What if it's some other system!?". Well, the only other system for teleporters I can think of would be... wormholes. And EVE has very strict mechanics for how those work. For an on-demand wormhole, you need two collaborative end-points - either two conjoined stargates, or a jump drive/bridge and a cyno. Yes, there are also 'natural' or 'spontaneous' wormholes, but we don't have any method of controlling those. Additionally, we've never seen wormholes on such a fine level that one might be used to pick up a single module, and not only does that end of the hole need to be meter-perfect, the delivery side also needs to hit the right spot.
So to pick up loot using a wormhole solution you'd need: Talocan/Sleeper/Jovian/Sansha level control of non-cyno non-paired wormholes, on an unprecedented level of fine detail and miniaturization. And that still doesn't do away with questions such as "Why can't I use this to tear apart the enemy from the inside, or teleport a bomb to their ship, or open a wormhole to suck out all the air to suffocate their crew?"