As you say, it is a convention to use the more "positive" word in Japanese. However, there are situations where we native speakers opt to use the "other" word. I could think of two conditions that make using the other word sound natural or even better.
1 Common knowledge:
This is when a thing's slowness, smallness, lightness, etc. is commonly known to the general public and the speaker decides that it can be used as a premise of a conversation. The slow speed of a snail （遅さ） is a prime example of this.
If you have to talk about the slow speed of a snail to someone who has never seen or heard of a snail, you would need to first explain how slow it moves. After explaining it, you can logically use 遅さ instead of 速さ.
Another example would be how "slowly" a Shinkansen train which is well-known for its high speed could run on a snowy day. It can actually run more slowly than a bicycle in certain places on a snowy day. In this case, you first explain the weather condition and you can use 遅さ with no problems or unnaturalness to the native ears.
Finally, allow me to correct your Japanese. You cannot say 新幹線の速さは何ですか as that clearly is a direct translation from English. You would say 新幹線の速さはどれぐらいですか、新幹線のスピードは何キロくらいですか, etc. Since we are discussing 速さ/遅さ, I probably should not be using the word スピード even though it is the more natural word choice for us.