Reef is a solid way to capitalise on water dominance, but it's not unbeatable. There are many factors that make it a great units:
- cheap for a strider, but has strider level attrition.
- free units!
- can affect land-bound opponents but does not fear them.
- drones have effectively twice their normal range (give or take), due to attack ground exploit.
- similar to funnelweb, very safe and reliable attrition.
- free small anti-nuke, has smaller range, but usually any threat of reef is enough to dissuade nuke, and it's a massive win if you intercept.
- multiple means of attack (free more resilient impaler).
- wrecks even razors by baiting them open then hitting them with artillery
- very few weaknesses.
- rearming wyverns and thunderbirds close to the front line, and wyvern has a tendency to absolutely wreck opposing hovers (until flail) and especially ships (until forever).
- is pretty mobile and therefore resilient to artillery.
- is cloakable and therefore resilient to bombers and tac nukes.
- has own radar for good measure.
- one of the few things that kills DDM without enormous casualties.
- safe from many traditional anti-heavy units such as infiltrator.
It really has very few weaknesses while being difficult to stop, especially for the average player in big teams.
Firstly, they are unable to affect anything underwater, so they have a persistent vulnerability wherever they happen to be. A reef cannot survive alone in duck infested waters. Thus, the reef player must invest fairly heavily in controlling the thin ice on which they skate. Assuming an even battlefield, this means they must be able to protect themselves from 4100 metal in scallops (roughly 14) before they can field a single reef.
Secondly, while they're really good at grinding away at things from a distance, they need to be able to protect themselves against air. Particularly gunships. Banshees, rapiers, blastwings, black dawn, brawler, krow... these will all kill reef for cost if it's not well supported.
Thirdly, Big Bertha will kill reefs all day, and can be inland enough to be safe from their drones. Reef-users can combat this with eraser, or terraform (but gives up mobility).
Fourthly, has anybody seen typhoon lately?! It's a stardust that moves! Fast! With 2200 HP! Shiiiiiiiiiit. Typhoon busts are pretty difficult to stop. They're powerful and fast, and will hunt you down - tearing through your defenses like paper. The standard porc logic doesn't work for sea, you can't just put up skydusts or DDMs and be safe. You need urchins to hit subs, and while reasonably effective you can't afford enough urchins to stop a typhoon swarm
and a reef.
There're other counters too - halberd bust, silo, superweapons, raven stack, but I haven't used these so can't speak as to their effectiveness.
The basic principle is that even though all of the weaknesses of the reef can be mitigated, they cannot negate every single weakness simultaneously or for cost. If you produce the threat that forces the reaction, you can the use that threat elsewhere (hit their base with the big bertha for example). Many players aren't good at having several plans going at once, which means in big teams if someone makes reefs they're going to chew through unprepared noobs until a carry shows their face. This is a very powerful thing to do for a unit that is accessible to anyone.