Shouldn't be a big problem. The idea is to get the water to pass through the entire media. Having water pass at hte bottom on one end and out the top on the other. sealing with a gasket and nylon screws will be difficult but not impossible.
it should work, it just will not be as efficient as a vertical one. water is constantly forced through the media over the entire time the media is in the vessel. gravity helps this in a vertical orientation. in a horizontal orientation as the media is used up it could settle leaving open water above the media. the water can pass through the reactor and not go through the media.
do not get me wrong the lower pH will still cause the media to desolve it just will not be as efficient.
The fact that your media will will be less eficiently exposed will be far outwheighed by the fact that you have much more CO2 surface area exposed. After all you are using CO2 to lower the pH. The more surface area you have, the more CO2 will be dissolved in solution. It will work better than a cylindrical unit.