Because having the shops in base be separate didn't add any gameplay, and having secret shops does. It doesn't mean it's a good decision, but I think we can all agree that having 2 guys standing next to each other selling different shit because of the item limit is not actually adding anything no matter what your stance is. It's fine though, I expect dota defenders to be obtuse about shit like this. You are also fine to prefer one over the other, but yes, bloated and archaic are both words that describe most of the 'extra' depth DotA has. Shit like denies are so nonsensical in any way other than "that's how wc3's engine works" that it's literally baffling that people defend it, but there you go - dota fans.
Mark Rosewater the lead designer for Magic the Gathering writes an article and two podcasts every week all about design topics, and one of his main rules of design is that you need to make players want to play the game in the most intuitive and fun way for them, because it's counter to their fun when the correct way to play is fighting their nature. Killing your own units is basically the definition of bad design. It feels stupid, in terms of the game world it IS stupid, and it's completely unintuitive to new players - making it obtuse for no reason. This exemplifies the type of decisions that led Dota to where it is now. Yes, you CAN make the player care about killing their own units, but how about adding that gameplay to something else that they actually think they should be doing instead? It emerged because of a broken system in the first place, and something like that it should be your job as a designer to recognize and stomp out rather than encourage. Last hitting is already effectively the same thing from a gameplay perspective, but it actually makes sense and is what the player already wants to do.