The general way I handle equipment is pretty much how YS sets it out and so far it has not been much of a problem.
A character has pretty much automatic access to items/gear according to the chart of page # 322 of YS. Under the trapping 'Buying Things' located beneath the chart...
a player can almost always declare that his character has or can reasonably afford anything that’s 2 levels or more below the character’s Resources.
That is direct from YS (and mods/admin feel free to delete text quote if it is an Intellectual Property issue).
If a character has the Resources Stunt: Lush Lifestyle (YS155) then they can have automatic access to items equal to their Resources skill. Keep in mind though, this access is limited to items that are 'reasonable' for someone to have. Skill tests are still needed to get access to rare or restricted items. In the book, the example of a regular person purchasing an assault rifle was used. Now the Resources cost of an assault rifle is Good, but for a regular, non-military/police purchase, the restriction makes the item cost Superb. Which is actually fairly accurate, since a legally papered fully automatic ex-military M16 assault rifle is ~$16,000 last time I checked, which is over the Great range of Under $10,000.
One of the things which is important with the declarations players are able to make about equipment, is that the declaration has to pass the reasonable 'smell test'. For example, a player with Resources of Average (+1) can normally make an automatic declaration that they have with them a common hand weapon, like a knife, baton or baseball bat (again from YS322). However, unless one is involved in security and/or law enforcement, making a declaration that a character has a knife with them in a courthouse, or an airport terminal ceases to be reasonable.
In the specific example of a character 'always' wearing body armor... The question which immediately springs to mind is, what kind? There are six different basic body armor classifications as set out by the NIJ here
http://www.ncjrs.gov/pdffiles1/nij/183651.pdf. If someone looks at a source for police body armor like Galls here
http://www.galls.com/easearchresult.html?question=Body%20Armor&searchaction=1&path=All%20Products%2F%2F%2F%2FUserSearch%3DAll%20Products%20%3B%3B%20Venture%5Fid%3D503185%2F%2F%2F%2FGear%20%26%20Equipment&resultsperpage=20 then except for the lowest levels of protection which also might only cover the torso, body armor is not exactly covert/concealable. Now if your player has a character that is an FBI agent, then the normal clothing for them would usually be something business appropriate, a suit or business casual clothing. The idea being that an agent (or a detective/plainclothes officer for that matter) should blend in, not be garbed in a fashion which screams "COPS!"
If your player insists on having his character go around all the time in Level IV tactical body armor (which would likely have been issued by the FBI), have the character's SAC (Special Agent-in-Charge) call the character into a meeting about appropriate behavior for an agent. If the player doesn't get the hint, then perhaps have them professionally assigned to a desk and/or sent off for 'psychiatric evaluation'
Now if a character wants to make a declaration about an item that would make sense to have, but not necessarily be sensible for them to have gotten it in time, etc that declaration is ripe for using an Aspect. I even have one made up that I'm waiting to use, "
Once an Eagle Scout, always an Eagle Scout" which plays up the nature of an Eagle Scout following the Boy Scout motto of "Be Prepared".
