Hopefully my experience will help you all out;
I operated a vacation rental within the city limits from 2013-2015. I was registered to pay sales tax to the state and TDD tax to Palm Beach County. Like you I could find no prohibition on STR in the Boca muni code so I began operation of my rental. I was shut down by code enforcement who found me because I was registered to pay those taxes.
The section of the city ordinance which was sited to me is Section 28-339- permitted uses in a residential district (see attached screen shots). The city code lists permitted uses in a residential district and their contention is that anything that is not listed as allowed is in violation. They go on to define what a "motel" is; the city's defiinition of a motel is not what we would traditionally think of as such (see attached screen shot. In the eyes of Boca Raton, a "motel" is a SF dwelling used for transient stays of less than 1 year.
Since "motels" are not a permitted use in a residential district- no STR in a residential district.
The ban on vacation rentals is not what they prohibit, but rather what is not permitted- a subtle back door kind of ban.
After I was shut down by code enforcement I was told I faced a $1000 per day fine if I continued to operate as a STR. Additionally I had to remove my listing with VRBO and dismantle the web site I had set up for my house. I chose not to fight this in court as it wasn't worth the time or effort for me. I did voice my concerns that the ban was only enforced selectively as many other rentals were operating on both VRBO and Airbnb. I was told that code enforcement was understaffed.
Fortunately one of my short term rental clients has become a seasonal renter for me and rents my house for 8 months a year.
So be aware that if you operate as a STR in the city your are subject to being shut down.