That's the thing with a trap deck. If you only play Junebugs, the runner can compensate by just overdrawing before running every time, and your trap won't be as effective. You are still forcing him to dump cards, but that only really, really hurts in early and maybe mid-game.
If you want to play a trap deck, you need to play other traps as well. Throw in a couple Agressive Secretaries or Ghost Branches (if your deck is built to leverage tags). Runner sees Junteki, gets cocky. Draws up to six cards and runs on that remote server. Hits aggressive secretary and loses most of his rig. In the end-game, that can be all it takes to win if the runner has cycled through enough of his deck.
Also, personally, I like to advance an agenda up to 3 or 4 counters and then let it sit there sometimes. Runner becomes convinced it's a trap because I stopped advancing. A round or two later, I score it. HUGE gamble, but when it works, it totally puts the runner off balance the next time I do it. Kind of like installing a card in a new remote server and advancing it twice even though you have a perfectly good remote server already setup. If you always put a trap there, the runner will never fall for it. But do that with an agenda once, and the runner will start to doubt himself.
You just have to mix it up. If you always follow the same pattern, your trap decks will fail every time.
And now that the data packs are adding agendas that benefit the Corp for over-advancement, the potential for mind-games has gotten even better.