There is no way to organize or hide elements from the Effect menu, although this exact issue has been addressed sometime since the older version you’re running. The current release of After Effects splits the Effects menu into columns so it doesn’t run off the bottom of the screen.
Here are a few other options for getting to Effects quicker than drilling through the menu system:
1. Use the Effects and Presets panel, which a tree similar to the Effects menu. The hotkey to bring up the panel is Ctrl+5. If you then hit Ctrl+F for find, you can start typing the name of the effect you want, and the list will instantly filter. You can double-click or drag and drop to apply effects from the list.
2. Use a third-party launcher. I use Video Copilot FX Console, but there’s also Quick Menu (and probably several others). This way of working is so fast, you will never want to use the menu system again.
It’s possible that right-clicking the layer you want to add effects to, then selecting the “Effects” submenu will break the list into columns as I mentioned above, but I’m not sure what version that was added.