Hydroponic systems, whether homemade or store bought, suffer from a few common problems. These problems include algae growth, leaks, clogs, inconvenience of use, the temperamental nature of some systems, (which make them high maintenance), and the expense of maintaining and reusing different types of systems.
Every hydroponic gardening system uses water and plant nutrients. Unfortunately, wherever you have water, nutrients, and light you will eventually have algae growth. This is a big problem because algae attracts fungus gnats, and fungus gnats will damage the roots of your plants. To prevent algae, a hydroponic system must limit the exposure of the nutrient solution to light wherever possible. The nutrient reservoir should be made from a dark or opaque material. The nutrient reservoir should have a lid. Holes in the reservoir lid should be no bigger than the hydroponic pump hose and the water return pipe.
The system itself should be relatively light proof. The weak spot in many systems is where the plant holes have been manufactured in the system. Plant holes should be no bigger than necessary to hold the growth medium (i.e. a netted pot or rockwool cube). If the growth medium is being watered from above, such as with a drip system, a cap should be used over the medium to minimize the exposed area. Drip emitters can also be made to run underneath a light proof cap, but this will prevent you from seeing drip emitters that have clogged. Any plant holes not being used should be capped or covered with dark or opaque material.
High pressure systems are more likely to leak than low pressure systems. The most common source for leaks in a hydroponic system are stab fittings and drip/spray emitters that slip out of position. Less often, root growth can cause leaks in a constantly flowing system by causing water to back up and spill out when there is not enough room in the tubes.
During a power failure, I once witnessed all the nutrient solution drain from a system back into the nutrient reservoir- which was about 10 gallons too small. I have also seen a high pressure pump that was not connected tightly enough suddenly blow off it's exhaust hose and soak down the room. Many leak issues can be avoided simply by using a hydroponic system designed around a low pressure pump, such as a NFT system or a DWC system. Further leaks can be prevented by using a nutrient reservoir large enough to hold all the water in your system, and by using pipes large enough to handle the systems water flow even after significant root growth.
Clogs cause the most problems with drip systems and spray systems (including aeroponics). Drip/spray systems use high pressure pumps to force nutrient solution through very tiny openings. Nutrient filters and pre-filters can reduce the occurrence of clogging but will not eliminate it. If you choose one of these systems, be prepared to spend extra time each day checking every spray nozzle/drip head and replacing any that have stopped working.
How easy is it to clean a hydroponic system in between uses, and how easy is it to do a nutrient solution change while the system is in use. An "easy to clean" system offers easy access to every surface inside the system, either by hand or with a brush. A system can be a headache to clean if there is no lid and the holes are too small, or if there are tight corners or unreachable bends.
A system should be easy to empty of it's nutrient solution, and the process should disturb the plants/plant roots as little as possible. A system should retain very little of it's original nutrient solution when emptied. The whole nutrient solution change should only take three or four minutes, assuming you have a reservoir of room temperature water ready to replace the old nutrient solution (plus a few extra minutes to check and adjust the new solution).
The main concern here is how much time you have to spend checking and babysitting a particular system. Every system will need it's nutrient solution checked and adjusted at least once a day, but some systems need to be checked much more often to prevent other problems. Drip systems should be checked two or three times each day to make sure the emitters have not clogged- a few hours without nutrient solution could kill a plant (especially in a fast draining medium).
The same is true for spray systems, especially aeroponics. If you are using no growing medium at all, then your nutrient solution drains immediately into thin air. No medium means no buffer zone protecting the roots of your plants. If a spray nozzle clogs in an aeroponic system, your plants could die in less than an hour. I suggest checking aeroponic systems four times a day or more, not only to check for clogged spray heads but also to check for broken pumps and power failures (which would be equally damaging).
The most reliable/least temperamental hydroponic systems are DWC systems and NFT systems. These systems are low maintenance and need to be checked only once a day.
One of the main expense with reusing a hydroponic system comes when you have to replace all of the grow medium. If you are using rockwool, for example, you have to throw out all of the old rockwool and replace it with new rockwool for each new crop. This can easily be a $100.00 expense (or more), even in a small system. Other systems use netted pots filled with expanded clay pellets, lava rocks, or other reusable grow medium.
Another solution is to use a DWC system or NFT system, which use very little grow medium and mostly grow the plant roots in standing nutrient solution (with air bubblers). These choices not only save you the headache of having to dispose of the old grow medium... over time, they also save you a considerable amount of money.