I've tried to find a better air filter system for my 94 f150, but seems like there aren't any. Most new ones have the one hose coming out to the filter, but mine has 2 going into the filter box.
Would it help or hurt if I drilled holes in the top of the box to allow more air ? Or any suggestions would be helpful

 

It would hurt. You'd be allowing unfiltered air to be sucked in to your motor. Keeping a clean air filter is the best thing you can do.
The truck already has cold air induction. It's slightly restrictive but sucking warm underhood air is not a benefit.
If you can work out a less restrictive induction system that still pulls air from outside the (hot) engine compartment then you will increase efficiency.
IMHO

 

You can use a k&n rf-1012 and do a few mods to get it to work. They also sell a rather expensive kit that includes that filter, but honestly, you can make it yourself with some hardware.

I purchased one of the kits off of craigslist for $50. The filter was dirty and needed a few cleanings but when it was done I have to say it was definitely one of the best mods as far as throttle response and engine sound. It made the engine sound like a V8 should sound. And it looks friggin cool

 

I ordered my RF1012 from Oreilly Auto Parts for $45. The price has since gone up a little, but for what its worth and not to start an argument, the throttle response gain from the large K&N are great. I've noticed ZERO downside to my warm air intake. At highway speed, the intake temp is the same as outside air temp. Ask me how I know.......I installed an intake temp sensor. No air filter setup on our trucks is going to hurt performance from a temperature stand point. The advertized 20hp gains are bogus and K&N mistakenly posted the dyno numbers for a 9th gen 5.0 and took them down after they realized that they showed zero gains. The dyno does not show the throttle response, which is better. Good luck either way.

Edit.....let me add, there was a long argument, and I spent 2 months with engine builders and two performance shops discussing temperature effects on our stock motors. To the best of our figures, we came up with approximately 1/2 (.5) hp loss with a warm air intake. However, there is the eco crowd who make the valid point that warmer air takes less heat (fuel) to combust. For what it's worth, i can get 21mpg all day long with my 4.9 at 55-60mph on the highway. That also includes a bunch of other mods including the electric fans, warm air intake, good maintenance and full synthetic fluids from front to back.