Low-height microwaves are not more or less energy-efficient than other microwaves. In most cases, the power of a microwave is the most influential efficiency factor, rather than its design or manufacturer.
Microwave ovens tend to have little variance from one another in terms of energy usage, which is one reason why the U.S. Department of Energy does not certify any particular microwave as an energy-efficient appliance as of 2015. However, a low-height microwave oven may be more efficient than other microwave models if it has a lower power rating. Microwaves with 800 watts of power or less are likely to be more efficient than those with 850 watts of power or more.