The high score system could have some meaning if taking respawning objects/killing respawning enemies didn't count. And automatically disqualifying you from the high scores list if you use cheat codes, of course.

Another thing to fix the point system, is that you should only get the score once, so if you purposely die to collect more points in the same place, you won't get them.
Or once you die, you should lose the points you gained, with the start of the level/checkpoints saving the score you had at that point of time.

To be a cheap person, you could always look up the levels in JCS to find all the secrets, though.