Yes, you should. If it is time for your baby to eat, or time for your child to get up, you should wake him up.
I wake both of my kids up quite often. I still have to wake Brayden, my nearly 3 year old, either in the morning or from naps, sometimes both. If you like consistency to the schedule from day to day, you will definitely want to wake a sleeping child. If you don't really care, then you could let it vary a bit, assuming your baby is old enough to do that.
You want to wake a baby in order to feed often enough. You want enough calories to get into his little body in the day that he won't need them at night. You also want to train his metabolism. If you eat at the same time each day, you get hungry at the same time each day. You want to wake a toddler just to make sure he will go back down in time for bed.
Sometimes it is hard to wake the baby. A couple of weeks ago, my son would not wake up from his nap. I gave him an extra 20 minutes and tried again with success. Also, you might need to use some creativity when waking the child. For example, some days my son is quite cranky when we wake him from a nap. If we read him a book, that usually solves the crankiness problem. He has only in the last six months started to be cranky sometimes upon waking. Kaitlyn (12 months) still wakes up cheerfully (though sometimes quite confused).
And yes, there are times you want to let your child sleep a little extra. Say naptime started late for whatever reason. Or perhaps an earlier nap was disrupted, or yesterday was hectic. Maybe you are going out that evening and need him to stay up a little later than usual. You can always make exceptions to your schedule to accommodate you, your child, and your family. But if you are following the Babywise program, then yes, you will often wake a sleeping child, and that is okay. Whenever I am waking up a cranky Brayden and am tempted to just let him sleep, I flash forward to his teen years and know I need to establish now that his parents have the authority to tell him when to wake up.