Have done any soil testing or build studies so that you can transfer the land in a more opportune way than when you bought it? 

There is a good chance the walls sit on bare soil and do not have propper footings underneeth. 

Some friend has been telling me foundation issue is common in Houston area because it is building on active soil, and the extreme weather might cause foundation issues here and there.

Be careful with the foundations, the soil is sandier so it's common for shifting to occur which will affect the plumbing. 

Only S-Corps can own other LLC's and it makes sense to have all the rent and other things roll up in one S-Corp and underneath your properties are just sitting in separate regular LLC entities.I am sorry that I did not go into that detail. 

Is the soil to sandy or swampy to build on? 

a) Keep the carpet until it is done. b) consider using engineered wood instead of LVP...yes it's a little bit more $$ but adds a lot of class and better durability.As @Lynn McGeein correctly says, LVP will absolutely allow liquids to seep through the seams and get underneath to the underlayment.

In today's lawsuit-trigger-happy society, asset protection is actually a small price to pay as opposed to having my company dissolved or ripped out from under neath me.  

When installing new ones in a gut reno, run the finished floor all the way underneath them, so if there is a leak, if flows out and can be seen and fixed, vs. soaking into the subfloor and rotting it. 

Virtually all basements are going to have water concerns, whether from high water table, moisture attempting to move from soil to concrete/concrete block to air, actual infiltration from walls, etc.