Here are my thoughts on particle and sonic weapons. As ever, take a handful of salt.
PARTICLE WEAPONS
The gauss weapons in TFTD are particle weapons, which means that they accelerate particles to extreme speeds and launch them. Particles don't have much mass but plenty of energy, so they would be a bit better than bullets for raw damage and push, and most likely would have EMP effects if there was anything left of the target. Probably sucks up tremendous amounts of energy, and is fast enough to approach the speed of light (300,000km/s). To put it bluntly: way better than bullets, lasers, or plasma. However, the power requirements are large enough that I don't expect to see a prototype particle weapon becoming available for at least four decades. Lasers and plasma weapons are currently being tested, though the latter is extremely impractical because we would need better magnets and power source in order to make it small enough for use by vehicles and people.
As to the effectiveness of particle weapons underwater, I am guessing it wouldn't be good.
SONIC WEAPONS
Sonic weapons on the other hand...I think their effectiveness is variable, according to what harmonics are used in relation to the target. A human and a lobsterman are very different, in that the former is quite fleshy while the latter is largely comprised of a plated exterior. Against humans, you can use a variety of settings to cause different effects - for example, distorting vision by shaking the eyeballs. However, what works against one material might not be effective against another. Bone, flesh, blood, metal, all have different properties. As such, in order to be effective against various aliens and their craft, it would be required to collect corpses and material samples in order to create "profiles" of ideal weapon settings for disabling or killing specific targets.
So instead of having a "kill" or "stun" setting, you would probably have to pair up one of these key words with the target that you are dealing with. For example, "Stun etheral". As you can probably guess, this makes a sonic weapon difficult to work with, because the operator would have to change settings according to what opponent is in front of them. However, integrating some form of AI and automated recognition into the weapon would remove this flaw.
One of the useful properties of a sonic weapon is that they may operate as a sonar. This can be very useful for identifying the location and possibly the species of enemy opposition. Unfortunately, it is likely that if you can hear the enemy through this method, they are probably hearing you as well. On land, sonar is likely to be much less effective, though terrestrial mammals like bats have demonstrated that it can be practical. As before, the settings for a sonic weapon would have to differ depending on what terrain it is being used in - water and air are very different mediums.
Sonic weapons are likely to have issues in the field when it comes to durability, because a big part of their function is effectively to shake. Ballistic weapons are built to withstand the heat and pressure that occurs when a bullet is fired - but a sonic weapon is likely to consist of delicate electronics, amplifiers, and other things that essentially makes sonic weapons into glass cannons. A traditional gun can be made out of durable materials like steel, but the inherent need for complex devices to generate and regulate sound is pretty likely to make a sonic weapon difficult to maintain. In order to resolve this issue, sonic weapons would use an ammunition system - whenever the ammo breaks, it is time to replace the cartridge. These cartridges would have to be designed with safety in mind, paired with a guaranteed number of uses in order to ensure that soldiers switch the cartridges. To not do this would increase the odds of a soldier trying to use a cartridge when it is broken, which is bad because it can misfire or simply fail.
+Variable effects, can be used to stun or kill enemies.
+Good range in underwater combat.
+Capable of making a "wide" or "narrow" shot. The former is ideal against multiple enemies of the same type in front of the user.
+May disorient enemies.
=When fired, the weapon damage is largely effective against the primary target and its species. Incorrect species only receive nominal damage.
=Can be used to detect and identify objects. However, enemies will also become aware of the user of this weapon.
-Fragile, the ammo cartridges are likely to break on the field. Ammo counter is unreliable, and a misfire or dud may result.
-Ineffective against unidentified enemies, as the weapon has to be calibrated for them. Data collection via corpse autopsy and material samples is required.
-Poor range on land.
As to the most effective weapon in underwater combat, I think that some form of torpedo or blaster bombs would be ideal. Water is simply a roadblock for most weapons, so the weapons would have to be tailored for that environment. In addition to this, water can block light with relative ease, making it difficult for humans to see at deeper depths. Some combination of sonar, infrared, mapping, and beacons would be necessary in order to navigate seabed battlefields.
