Yes, sir, it’s possible to maintain seahorses in a bare-bottomed aquarium if you wish, in order to facilitate water changes and maintenance, as long as the aquarium is equipped with an efficient filtration system that can provide adequate biological filtration minus the live rock and live sand. Remember, when you remove the live rock and live sand, you are not simply making a cosmetic change and rearranging the decor of your aquarium, you are also removing a very large portion of the beneficial nitrifying bacteria in the aquarium. The porous surface and interior of the live rock support a vast population of beneficial Nitrosomonas and Nitrobacter bacteria as well as a large population of anaerobic denitrifying bacteria. These are the bacteria that carry out the nitrogen cycle in the aquarium, converting poisonous ammonia to nitrite and then converting the nitrite to relatively harmless nitrate, which the anaerobic bacteria in the interior of the rock then convert to nitrogen gas that eventually leaves the aquarium.
Likewise, the live sand provides a tremendous amount of surface area with its millions of tiny sand grains, which also support a huge population of these beneficial nitrifying bacteria. So when you take out the live rock and the live sand, your aquarium will be losing a very large portion of its biofilter in the process.
You will need a very efficient filtration system on the aquarium to make up the difference. A wet-/dry trickle filter or a biowheel filter that can support equally large populations of the beneficial nitrifying bacteria should be in place before you consider removing the live sand and/or live rock from the tank. And you’ll want to make sure that your 50-gallon tall tank is equipped with an efficient protein skimmer that can remove dissolved organics before they enter the nitrogen cycle and thereby help to maintain good water quality.
So make sure that your aquarium is equipped with a well-established, very efficient biofilter and a good protein skimmer for supplemental filtration before you consider removing the live rock and live sand. And once you have removed the live rock and live sand — taking away a substantial portion of the biological filtration ability for the aquarium in the process — be sure to a monitor the ammonia and nitrite levels in your seahorse tank very carefully for the next few days and weeks. The tank may well experience ammonia or nitrite spikes while the biofilter is adjusting to these changes, and you may need to perform major water changes in order to prevent the levels of ammonia or nitrite from presenting a danger to the seahorses in the meantime.
As long as you maintain adequate biological filtration throughout the process of removing the live rock and live sand, then it will be fine to maintain a bare glass bottom on your seahorse tank, if you prefer. But the seahorses will not be comfortable in the type of bare tank that works well for breeding pairs of clownfish. The seahorses require plenty of hitching posts and holdfasts to provide them with attachment points and adequate shelter if they are going to do well in a bare-bottomed aquarium.
A certain amount of complexity is desirable in a seahorse setup. For example, a tank with too few attachment sites and hitching posts is a stressful environment for seahorses, as is a sparsely decorated aquarium that leaves these secretive animals feeling vulnerable and exposed. Such sterile environments are commonplace when seahorses are being maintained under laboratory conditions. A Spartan setup facilitates feeding, water changes and maintenance, in general, but it can adversely affect the behavior of the inhabitants and may even prevent captive seahorses from breeding.
Hippocampus relies on camouflage and remaining hidden for its very survival. Seahorses can thus become distressed and agitated if their tank is too barren to provide adequate cover. This is particularly true during courtship and mating when the increased activity level and heightened coloration make them highly conspicuous and vulnerable, and breeding may be severely inhibited under these conditions.
A recent research project that studied the behavior of captive Cape seahorses (Hippocampus capensis) recently confirmed the need for a certain level of complexity in any setup for seahorses (Topps, 1999). The study found that seahorses display more "natural" behavior when they are provided with an elaborate, structured environment that includes a number of different microhabitats (Topps, 1999). These findings are another indication that a sparse setup with inadequate shelter can inhibit the behavior of captive seahorses.
So it’s just fine if you want to maintain a bare-bottom seahorse tank, Sean, providing you manage the biological filtration properly, but you don’t want to have a completely barren seahorse setup. A bare glass bottom is fine providing you have plenty of artificial corals and/or plants to provide the seahorses with adequate hitching posts and a sense of security.
Best of luck redecorating your seahorse tank so that it’s more to your liking, sir!