So I have a project to build a machine for pulling fishing nets over a boat. For this I will use an electric motor and go-kart wheels.
The perfect physical size wheel hubs to use are for rear wheels 25mm axle, 40mm hub and shorter in length than the front hubs I can find, but I need the smaller front tires and front rims. Axles will be DIY.

So the question is: if both have 25mm axle and 40mm attachment, will go-kart rear hubs bolt securely to front rims or will there be issues?

dude nobody knows wtf you are talking about.
here's a nickel's worth of free advice:
when you want to nigger rig a bunch of bullshit together that was never intended to go together and use it in a manner that it was never intended to be used in, chances are it's not going to line up/bolt up/work quite the way you want it to, if at all.
you're not going to dump an amazon go-kart kit out on the floor and an automatic fishnet-reeler-inner just magically happens.
you're probably going to have to take measurements. you're probably going to have to bend/twist/cut things. you're probably going to have to drill/ream/tap/mill/turn things. you're probably going to have to think a little to make it happen.
but don't worry, anon! it's not as bad as it sounds! there are literally millions - yes, millions! - of men that have been frying their brain cells with drugs and drowning them with booze for decades that could do something like this.
you're not stupider than a drug-addicted alcoholic that mixes cement for a living, are you? of course you're not!
so, hop to it, anon. we have faith in you.
post pics when it's done.