No secrets here. As mentioned above, I've been making a perfectly clear honey-sweetened limoncello at Letterpress Distilling for ten years now.
Like OneFootKev says, it's not easy and it's not cheap.
This is my process:
1. Make a honey syrup (honey and water) and heat it to 160F before adding it to the spirit; this actually changes the structure (denatures) of the proteins so that they'll precipitate even faster and much more cleanly.
Blend the honey syrup with the spirit well.
Chill the product. Like, REALLY chill it. Depending on your volume, you can chill it in carboys in a chest freezer (we used to do this) or in a tank with a glycol chiller (we do this now). Basically, the cold temps will cause the honey proteins to crash out much more quickly and cleanly. Then chill it for a few days. In a freezer, 2–3 days will do it. In a glycol tank, we let it run about a week. Then we let it come back to room temp, at which point the now-separated proteins will either float or sink (we can't figure out why it does which, but they almost always float). Then we slowly open the bottom of the tank and rack out the clear stuff (if it's floating) or the goop (if it's sinking).
Once we have as much clear product as we can get and the proteins start to creep in, we collect what's left separately (we call this the dregs) and then put those in chest freezers to separate again.
See the attached photo for the end result.
Hope this helps some folks.