The incremented abilities of your units are still valid (as for the abitlities of weapons).
Auras and Stratagem cannot target or affect anything inside a transport (yours or enemies) even if it is open top.....something i would really love to be changed in the next codex.
But yeah, inside an open top transport, your poison weapon will still be poison weapon, etc....
But you can't use the reroll aura of Archons for exemple nor a stratagem.
Hope this will help clarify