Your title is slightly missleading. Let's clear this up.
1-
40% bonus AD means:
(Total AD - Base AD) * 0.4
2-
140% AD means:
Total AD * 1.4
You can also have
3-
40% AD AS BONUS DAMAGE
Which means:
Regular Damage (usually an Auto Attack, so Total AD) + Total AD * 0.4
AND
4-
40% Bonus AD AS BONUS DAMAGE
Which means:
Regular Damage + (Total AD - Base AD) * 0.4
The first is usually put into abilities. For example, Shaco's E, at level 9, deals 210 + (100% bonus AD) + (100% AP). It means that the ability will deal it's base 210 damage that can be amplified
by building either AP or AD, but won't benefit from his base AD. It's worth noticing that there is no such a thing as Bonus AP, as all AP is Bonus AP.
The second usually indicates how much damage a modified auto attack will do, like Rengar's and Xin's Q. It uses both the base AD of the champion and any AD he might have bought during the game.
The third works basicly as the second one, with the only difference being the way it's worded.
The fourth is usually put on Auto Attack modifiers on champions that are expected to build lots of AD. The reason being that it completely ignores a champion's base AD, requiring him to buy AD to be effective, but that is more about game design than your post requires.
To answer your question regarding Yorick:
Both listing it as 140% AD or listing it as dealing 40% AD as bonus damage means the same.
Note that there is a big difference between Deals 40% AD as bonus damage and Deals 40% Bonus AD as bonus damage, as bonus AD does NOT take into consideration the base AD of the champion.