When you upgrade the shears they cause less damage to the plants. With the L1 shears, if you prune a healthy branch, leaf or flower, there will be a big reduction in health. With the upgraded shears that doesn't happen.

I've discovered that with practice I get better at using the net, so when I upgrade I don't notice a lot of difference. But after playing for a while in a game with the golden net, if I start a new game and I'm back to the green net it is more noticable. bugs that I was able to catch before are harder again and/or I'm feeling more clumbsy with the net.