On our last trip 4 years ago, my youngest was 3. She was just under 40" and wasn't able to get on any of the 40" rides. We prepared her for it and she was ok with it, but it did make the entire trip much more difficult since my boys (ages 5 and 9 at the time) wanted to do whatever thrill rides they could get on. She never cried (at least not about that) and didn't throw any tantrums. With the exception of one unrelated incident she was great the entire trip. But it was clear that she really wanted to go on those rides.
For whatever reason, I somehow managed to get her on Splash Mountain twice and she loved it. The first time the attendant at the top felt bad that she was so close and let her through and the one at the bottom never measured her. The second time nobody at all measured her. If there was a harmless way to get her to be a half inch taller I definitely would have done it. She would have had a much better time and my wife (who insisted on staying with her) would have had a much better time.
This time around she's about 48.5-49 inches without shoes so Disney isn't a problem. She'll just have to miss a few rides at Universal. Having all your kids height eligible for the rides you want to do makes planning for the trip and the trip itself much easier.
I just don't see anything wrong with trying to get your kid that extra quarter to a half an inch so that he/she can go on as many rides as they want.