I have recently ran my party through two adventures that give the acolytes the options of attacking and destroying door to gain entry to an area or attack an object to render it harmless(Jurisdiction from Book of Judgement, and Tattered Fates respectively) My questions is how do you handle attack these objects, unlike cover, they are given wounds to represent when the object is breached or destroyed as well as an AP number. Do they get any bonuses to hit, is it considered helpless (I.E. auto hit with additional d10 of damage)?

Any opinions on this would be welcomed, Thanks.

I assume they just have an armour value and/or a toughness value, and any damage beyond those values renders them inoperable/open/ruined. the 'EoD' campaign had a door-lock that required 12 points of damage (in a single hit) to open, but in the same way you could say it has an armour/toughness of 11, and so therefore MONO weapons would go through doors and locks easier. (the AP for cover is a good way of gaguing required damage, metal is 10-16, concrete is 32, wood is 3-5.)
A tarantula sentry might be different, I think it's in the Lathe Worlds' supplement, but otherwise i'd treat one of those like a stationary vehicle and use the vehicle rules.