I suggest to remove short pipe variant, it's really annoying to have too much entity that doesn't really serve any strong purpose. Yes they cost less but that really not a big deal in factorio.

Less is more.

If this was my mod, I might agree with you. But this is the opposite kind of situation to filter inserters, where Deadlock added short variants despite the base game not having any. So they're definitely staying in the main Patchset. Plus, if I removed them, someone else is going to come along and ask for them to be put back in.

I could make a "Long undergrounds only" add-on to this effect, but I have a better idea:

The underground pipe icons are not easy to tell apart, so why don't I make a "Pipe overlay icons" startup setting, like Inserters have? Water, steam and air pipes would have their corresponding overlay icons on them, and the long undergrounds would get the red arrows from long inserters.

I love short pipe :D So would you use one graphic for all pipes with different overlays?

If it were like that I wouldn't like it, IR3 is also beautiful to look at not only to play, compared to the vanilla game it's on another level

I really think less is more, and I really encourage you to reconsider, there already A LOT of new entity and adding useless entity is just noise, a lot of overall mod do this mistake and while I think IR3 is great there is some pitfall, and this short pipe is one of them; if it was two separate network that would also the have two underground pipe that doesn't connect to each over I would say okay but no, short pipe connect to long pipe, it's just totally useless, and it's too easy to confuse them.

There is a reason to why base game never added short pipe and there is a reason why base game removed filter inserter. Understand the why behind these choose will increase quality of IR3

Thus if you give me an option to disable them I would be happy enough

You know what, IR3 has enough startup settings, one more couldn't hurt, right? Implemented in 0.4.0.

The selections with the initial settings always make everyone happy :D

I think short underground pipes are really necessary, at least during the steam phase. Components are too expensive otherwise if there were only long pipes. But if it's a toggle, that's nice.