Beds with storage integrated underneath them are often discouraged because sleeping on top of ‘clutter’ can negatively impact the flow of energy. For example, there are some things not to store under the bed, according to Feng Shui, because they can make it harder for us to rest.
That being said, many larger bed sizes, such as king-sized beds, come with storage built in to make use of the amount of square footage they take up in a bedroom.
It is down to you whether you decide that having the clutter tucked away somewhere neatly is better for your energy than having it out in visible spots. Work around your needs and use Feng Shui as a suggestion to follow, rather than a strict rule.