Since there are different part numbers mentioned, I will go with some generic guidelines.
A good starting point would be the HSMI (Handling, Soldering & Mounting Instructions) manual of the product you are interested in (e.g. see BME280's HSMI manual here, you can find it from the product's page or Downloads page on our website).
Our environmental sensors are protected by a metallic lid, but features an opening hole to the environment. Water, dust, vapor phase soldering, cleaning agents, etc. shall not enter this hole and get on the sensor elements. If needed, the hole of the device could be protected against contamination during such processes by some silicone-free protective layer (e.g. kapton tape).
Using a protective vent/membrane in the field is common practice (often achieved at the casing/housing level) and should not significantly impact the measurements. Please avoid total or partial covering of the sensor by any protective material.
For the best performance, integration is key and it is therefore important to consider the HSMI's guidelines (position of the sensor, thermal (de)coupling, dead volume, air flow, etc.).
I am also considering a cleaning step for our PCBAs and our end product has a silicone gel layer surrounding the BME280. Can you clarify why the protective layer during the cleaning process should be silicone-free, and if our silicone gel layer in close proximity to the BME280 will affect humidity, pressure, or temperature measurements?
HTS221is the humidity sensor of ST not us, so i can't give any comment on this part.
I think you can directly use BME280 which has the humidity and pressure output directly.
The dust and water directly into sensor hole will damage the sensor, so in your water proof design, you need to consider to use membrane.
You can refer to the HSMI document for BME280 for system integration guidance.
For your other questions, maybe you can give me some more detail information what you are looking for.