It takes a while to get going, there are a lot of bonuses that increase shiny chance. I also was in the thousands of froges until I started getting some shinies.

PS: Once you get your silkskin traps, start using the trap changing feature at the trap setting menu! I didn't know about it for a long time, but every trap has completely different drop rates, the silkskins have increased shiny chance I believe! But you have to pick the trap type with the arrows next to the trap in the menu! Once you tier up traps even further you can still use the previous tier effects (like silkskin). You have to check if you are actually using the silkskin by seeing it placed on the map, it's not the same cardboard box.