Not gonna add customization on the spacecraft, it is too complicated.
There are already upgrades for the weapons (damage,accuracy,type), shield and energy-core ... they (the recipes) are just not yet unlocked ... hull upgrades and the right weapon are glitched/bugged right now (v0.26) ...
The decontamination bay is a good idea ... we all know the pleasure of a hot(cold) shower after a stressful day of work ...
Maybe an activator (blue cylinder) near the landing portal or inside the lab ... automatically add and use a Cleaning Kit (lvl 1) plus a Clothing Repair Kit (lvl 2) plus a Purge Kit (lvl 3) and reduce ship energy by 5/10/15 units ...
Could that work ?