It seems that when I use bobber stoppers and peg the weight against the bait I have much lower hookup percentage. Is there something to this and is there anything I can do to improve hookup ratio.

What hook and bait are you using? And what action /power rod?

Large worm or beaver/creature bait. Usually owner offset hook. All star or Temple Fork medium heavy action. 20-25lb seaguar invisx

Use a straight shank hook

and snell knot

I don't worry about the snell. I have seen how it kicks out the hook- but I retie too often

understand that haha I get in a hurry and don't do it a lot of the time

I don't like the stopper at all. It is a rubber bumper in front of the weight and will drag over a limb just enough to feel like a bite. I do not feel for the bite. I feel for resistance. When it is grabbing everything under the water that is resistance. I use the peg-its with the round ends on tungsten weights. They have a slit in them for the line to rest in which centers the line up on the weight. They are easily installed and removed from the lead weight when changing weights. I always peg when fishing heavy cover on T-Rig and also on my C-rig because I don't fish deep with the clacking sound technique.

I love a bobber stop. I slide it about 2" above my Texas rig sinker.

Helps get a lot of hang ups lose in brush piles.

Use a sraight shank flippin hook.

been pegging mine for 30 years with a round tooth pick.push it in from the bottom firm and break it off slide weight back down against worm.

Same here. I use "Peg-its".

a peg it makes the line go through the weight off center... I only use bobber stops. easier, cheaper works better in my opinion. It is more weedless imo as well