so I've invested 500 gold into a few shops then sold them all my stuff till they had 0 gold

and then i waited 48 hours and then they had the gold amount they had pre investment ...

whats even point of investing if gold comes from my own pocket and doesn't permanently boost there gold stock ?

why don't i just buy an item from them worth 1000 gold and sell it back for 500 ...

It should permanently boost their funds. If it doesn't, you're glitched somewhere. As well, the results of those increased funds perks/investments are cumulative, meaning if the vendor is starting at 750 and you invest 500, it goes to 1250 and then if you take the 1000 perk, it will go to 2250. And yes, it's very handy for someone who finds his hands full of things to sell after walking down one of the city streets. Oh, wait, also need another perk there...

well ive only invested in the blacksmiths so far and they tend to start with 1110 gold for a very very short time they were at 1610 gold

never invested in any play-through and the merchants i constantly use have all gone up to 3k , one or two to 5k. Gave me the impression the more you use a particular merchant, the more they like you and the greater their pool of gold. The investment perks are kinda a waste, i mean just by selling junk and crafted items you dont need you end up with way more cash than you will ever need. I suppose if those perks are taken earlier it makes a marginal difference, but in a game where the economy means nothing and you will be rollin in septims by mid level whats the point?