That shouldn't be the case. Stereo microscopes which have two objectives and two eyepieces so that each eye sees a separate image are almost always designed for top illumination: sometimes exclusively and other times they have the option for both. In biological circles they are sometimes called dissection microscopes. Binocular microscopes with a single objective present the same image to both eyes and are often only usable with bottom side illumination.
However, many microscopes don't actually come with any illumination at all. You buy your illuminator separately. The most common options for a stereo microscope would be a halogen fiber optic gooseneck illuminator or an LED ring lamp. The ring lamp attaches to the objective mount and is designed for the specific line of microscopes. They provide nice uniform illumination and are very convenient. Low quality ones may have poor color rendering due to low quality white LEDs. The fiber optic illuminators are less convenient but more versatile -- they can be pointed anywhere you need a bit of extra light, provide excellent color rendering while blocking the heat output of the lamp. Both tend to be expensive. On a tight budget you might have to make due with a desk lamp or an LED flashlight clamped into a vice.