The short answer is that it can be, but it's not usually a problem. Most modern HVAC systems are designed to work with higher Merv filters, so millions of homeowners rely on them without issue. The main risk of using high-efficiency air filters comes from the fact that they remain unchanged for long periods of time. If you're aware of changing your filters regularly, you're unlikely to experience any filter-related issues with your HVAC system. In general, filters with higher Merv ratings capture higher percentages of particulates as well as smaller particles.
MERV-13 is practically the highest rating you'll need for a residential home. Higher ratings are more effective and improve air quality, but they are also more expensive. Also, higher doesn't always mean better for homeowners. MERV ratings above 16 are commonly used in specialized commercial environments where air filtration is critical, such as hospitals. But for residential homes, anything above MERV-13 is overkill.
I'm wearing a MerVi cape and using a layer of Merv 1900 3M Filtrete on my mask (I made the mask as a cover so I could remove the filter to wash it). It turns out that sometimes, due to the unintended consequences of high MERV filters, the cure is worse than the problem. If you want to clean your air and handle dust, mold, pollen and bacteria, then a MERV 8 will do the job. The same goes for households with smokers or pets, as Merv 11 air filters are better at eliminating odors. Generally speaking, anything under a Merv 13 air filter should provide very efficient air purification in a house without affecting airflow.
Low-efficiency filters are typically found within MERV 1-4 and high-efficiency filters are MERV 13 and later. The MERV scale is not linear; the difference between a MERV 6 and a MERV 8 is almost double in the percentage of particles captured. If the Merv rating is too high to be operated by the oven fan motor or air handler, the result will be low airflow. Meanwhile, air filters with a MERV rating of 14 or higher are designed for commercial HVAC systems that can handle the coarsest filter material. Keep in mind that as the MERV rating increases, the filter becomes more restrictive and more pressure and energy will be needed to push air through it. This Merv filter is questionable for use in masks, as it will actually be effective for this use since it needs an electrostatic charge that it does not receive when placed in a mask.
Build the return so that it can house 2 Merv 18×18 tall filters side by side, giving you 648 SI of surface area for filtration.