Just taking your scenario and working off what you have so far.
A ship designed for space, is a lot different than a ship designed water. See this question and answer/S from SpaceExploration SE. A 'spaceship' is designed to withstand internal atmosphere pressure of 1 bar pressure to the outside and can be designed with no cross beam support and have very thin walls. While submarines have to withstand several to dozens of bars of external atmospheric pressure. They have much thicker walls and need some sort of structure support.
Now from what I can understand, these military 'water units' of yours don't have to be designed for space but it has to get from space down to the water! May I suggest a MIRV style re-entry method.
This was described as a Cyclon MIRV
What I'm envisioning is a hollow outer shell that is designed for space and more importantly the heat of re-entry. This could be tube shaped, cone shaped, whatever works best. Once through atmospheric re-entry, this outer shell can fall away revealing several of your water units. This 'thinner' outer shell would be no use to any explosive bombardment and any fragments might get caught in critical ship parts so I reckon best to lose the fake walls.
Your panelling and parachutes should still work. However, as I mentioned in my previous edit land based defenders would target your parachutes, panelling and balloons. You could possibly use the release of your fake walls as red herrings for any guided weapons coming your way, like chaff. Invest in Chaff!
You would aim to either land in the middle of the ocean with some distance from any land based defensive systems or have multiple, self deploying panelling and parachute replacements in case they do manage to destroy your already deployed equipment (I would recommend both alternatives). I believe you would have several to hundreds of these MIRV styled units deploying at the same time, simultaneously releasing your 'smaller' water units at calculated stages to reduce the risk of all of them getting hit by each other and by the defenders.
You can then have each individual 'water unit' split off from your MIRV increasing the chances of a ship getting through. More chaff would be necessary if under fire from the planet's defenders. These are the war ships built for atmosphere and water pressure. So they will be thicker hauled and capable of surviving hits from missiles and explosives (I hope!).
As previously mentioned, everything will have to be strapped in for a vertical entry. I think a roller-coaster styled harness which is fixed in place may be a death dealer for your troops. Rather have the harness on a 'elasticated' system, almost like bungy rope (but not that stretchy). IE a suspension system. This would lessen the effects of the sudden impact into the ocean while still keeping them secure. You could have several critical ship systems on a suspension system as well.
If you wish, you can design a secondary MIRV-like capsule that could encompass your 'water units' that would act as the suspension unit to the entire 'water unit' rather than just the troops - almost like a ship on an internal track system. But that is a lot of debris to take into account.
I know you mentioned that your panelling and parachutes would slow your speed down to that of lifeboats launching off oil rigs. You could combine this with this previous worldbuilding SE question regarding breaking the surface tension of the water.
I initially suggested that you consider shooting something 'large' into the ocean before you crash into it to break up the surface. Apparently mythbusters has disproven this on a human scale. However, you will be in a ship with a thicker skin than that of a human body. Seeing as you may be coming in under heavy fire, maybe some of your airbraking techniques failed to work to maximum effect so you would still be coming in too hot. The answer, to the previous linked question, by ckersch suggested that it is not so much breaking the surface tension but aerating the nearby water.
creates a localized downward current and aerates the water. The downward moving water reduces the velocity differential between the faller and the water, which in turn reduces the force exerted by the water on the faller. Aeration reduces the effective density of the fluid, which also reduces the force of the water on the faller. (In essence, the faller has to move less water out of the way per unit distance travelled if some of the water is replaced by air.)
You could design a 'cannon' in the 'bow' (front?) of the falling ships. These could shoot an explosive device into the water that would release a large concussive force aerating the water before the ships hit. Make sure that the ships aren't too close behind the explosive as you don't want to weaken your own ship's defences before you even start fighting your enemies!
You can then use the water dynamics of the water returning to normal effective density, along with your balloons to help propel your ships into your horizontal position. If there are defenders in close proximity to your water landings, your balloons are especially vulnerable. So, maybe consider a kevlar based material or again multiple balloons in reserve. You could consider using a substance similar to the spray filler for tyre punctures as a balloon's 'self healing' technique but I don't know how that would affect the landing qualities of the balloon.
Take a few minutes to take stock, see that all your troops survived and then you can decide how it is you wish to attack your land and possibly naval based enemies.
Mirv image from a osnetdaily http://osnetdaily.com/2014/12/china-tests-icbm-multiple-warheads-thanks-clinton-era-tech-transfer/