Hydraulic Bottle Jack is harder to move in and out under a vehicle and they require more space between the floor and the bottom of the vehicle for clearance. You can't even begin to fit a bottle jack under most average size vehicles as there isn't enough room under the frame.
Also, as you raise a vehicle up there is movement since the vehicle raises in an arc motion. A bottle jack is stationary and therefore it could result in the vehicle slipping off of the lift point or the jack tipping. Floor jacks often have wheels and can slide to prevent any movement.
Add to this that floor jacks have longer handles allowing for faster jacking action and that they generally have a larger range of motion (a 5" tall floor jack might have 15" or more of lifting height for example)... it just seems they are better for working on vehicles.
Bottle jacks have their purposes - but it is generally on heavier equipment or stationary uses such as raising a building or acting as temporary support for a structure. Floor jacks are just better and more efficient for working on the average vehicle, so that is likely why you tend to see more of them in garages.
And floor jacks are much faster/easier to use, IME. I have both (two of each, actually), and I almost never use the bottle jacks. (Last time I did was to compress the suspension on my Jeep by jacking the spindle while the axle was already lifted and on jack stands.)
Bottle jacks have there places but for shop use its always gonna be Floor Jack 3T , For the many reasons already discussed. Where bottle jacks come into play are for Large machinery anything over 5 ton its more economical to use considering a "Quality" 10 ton floor jack runs $2500 where you can get the same "Quality" 20 ton bottle jack for around $200 or less. Next reason of thought is, if you have a flat tire on a grain truck your not gonna pack a 500lb floor jack around with you. They have there uses and people who use them every day would argue that they are more handy than floor jacks.