Yes. Bonuses are counted as part of the wage bill in the financial reports. That is the same for us and all clubs. We have typically always been at or under 50% with our wage to turnover ratio.
New FFP rules look at combined wage and transfer fee spend (with agents fees included as part of the transfer fee). Many clubs in Europe will struggle with the new FFP regulations and I'll be interested to see how that unfolds and how heavily UEFA punish those who do not apply. We are quite well placed for the new regulation (though missing the CL will definitely have an impact on our transfer budget).
Unfortunately we have now missed our window for a high level of spending on the playing side of the club. The time to do this was a few years ago when we were the furthest under the FFP line of all clubs in Europe (we had a massive £400m of wiggle room at one point) though the club couldn't take on more debt to spend due to the high level of debt that the overspend on the stadium resulted in, it would therefore have had to have been done via injection of capital from owner or outside investment.
From a cynical perspective FFP always smelled like it was designed to keep the status quo while pretending to protect the game.
That said, the current model doesn't work, having state ownership or unlimited spending isn't a good thing for the game and no fan (other than the ones of those clubs) should want that. The problem will be if someone can actually spend like Chelsea is now (spending more than entire leagues) and can still make it fly under FFP, just like City somehow has more "income" than Real Madrid via interesting sponsorships, you really still aren't doing anything substantial.
Someone did a review of the proposed changes, it's over 3 years, Spurs is one of the only clubs in Europe that could get in line with the year 3 requirement at this point.