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There's something I didn't realize earlier...
Rebecca owns Higher For Hire (which she spent a LOT of money to acquire); and yet she has to pay for an apartment in town.
On the other hand, Baloo & Kit are living inside Higher For Hire, which is where they work but don't own the place.

It's a bit strange, but I'm guessing Rebecca probably didn't want to live in Higher For Hire (sure, she has a great view in her apartment )
And I'm betting she's loaning the room and taking this into account when giving Baloo's salary

On a side note, I think it'd be much easier if they were to all live at Higher For Hire (surely they could expand and make another room!)

Bosses are like that, they live above those they hire. I bet she sees herself as below living in such a place, snob!

And well they have to live somewhere, they're the securty for the place as well!

True to both things, yes
Well Becky may be a snob at first, but I still think she would change after knowing Baloo (and the opposite's true)

Of course, but it's common in some places. Sides she's no monster who'd leav them on the street.

There are several reasons why the living arrangements are they way they are. Allow me to list a few of them:

Plot perspective:
Having two distinct domiciles for two groups of characters allows them to pursue their own plot lines without necessarily having to involve the others. This way, Baloo and Kit can go off gallivanting at the writer's content without draggin Rebecca and Molly into the same storyline. It would eventually become problematic to think of reasons why a certain sub-set of characters in the same house would /not/ have knowledge of, or be involved in, a certain story or sub-plot. By keeping them apart, they don't need to forcibly interact.

Trope:
Talespin revolves a lot around the 'unconventional family' trope heavily favoured by Disney. To maintain the status quo, it is imperative that the protagonists of this dynamic do not constantly socially interact, or the trope would devolve into early 80's sitcom territory (The Odd Couple springs to mind).

Romance sub-plot:
The relationship between Baloo and Rebecca is kept intentionally vague. Had they been living in the same house/domicile, they would eventually be forced to face their true feelings in a romantic sub-plot that the writers were not willing to create. Likewise the barrier between employer/employee would fade into insignificance and with it Baloo's motivation to work at H4H. For their characters to maintain their distinction (alternating pro- and antagonist), they cannot live together.

Reality:
In the 1930's, with the Depression still a very vivid memory, the division between haves and have-nots was never greater. Business owners were usually living in opulence with their employees sharing squats or shanties at the edge of the city, unable to afford even basic rent on a single room. For employees to live on premises had three distinct advantages for the owner:
1) Free night time security
2) Ability to run the company at 'unsociable' hours because staff was permanently on hand
3) Employees living on business premises are less likely to make wage or work condition demands, as they rely on their employer for shelter
The living conditions for Baloo and Kit are, for the era, quite generous.

Notice how, in Plunder and Lightning, Baloo's Air Service lacks the most basic amenities, and Baloo and Kit are forced to sleep in either a chair, a hammock or the Sea Duck's emergency crew bunks. Shortly after taking possession of the property, Rebecca makes it habitable for her employees and intentionally provides them with a place to stay, taking it for granted that they'll do so. This underscores (in plot) her less visible caring side, though as mentioned previously this will be profitable for her in the long run underscoring (again in plot) her business sense.

In conclusion:
It's common in Disney cartoons for the main characters and main support characters to have a slightly unusual living arrangement. Characters which are not deemed to be wholly integral to every plot line will be kept strictly segregated for the sake of plot, and characters that are not to be romantically involved will never be made to live together. That said, there is a strong case to be made that these living conditions were pretty much the norm in the era in which Talespin is supposedly set, and that Higher for Hire actually offers a modicum of stability and luxury to its staff, while maintaining the contrast with the wealthier abode that is Rebecca's apartment.

Wow, I didn't expect such a long answer, but I have to agree with everything
Still, it would have been nice to see them living together for one or two episodes.

In "A Jolly Molly Christmas" they stay at H4H, don't know why, one some fanfic's say it that it happened not long after Becky's Apartment was damaged in "Mommy For a Day" or "It came From Beneath The Seaduck".

Well I still haven't watched that episode actually, but now that sounds great!

Yeah, that'd be nice to see them get closer! They're meant to be a "family"!