Are vias acceptable?
Vias are totally acceptable and used in almost any design, the most important things you have to worry about is the use of via's on high frequency lines and on power lines.
If you have a part which requires some higher currents or anything, say a design of a power supply for example, it is required you put several vias in the same line or in the same power polygon to be able to handle this current
Stack exchange current through via
The other problem with higher frequencies, is that if you have a multi-layer board the via can act as a stub, the stub can act as an unterminated transmission lines causing problems with your signal integrity.
More info about Stub and vias
To summarize: Vias won't increase production cost (unless you do special operations like blind vias or back drilled vias and are used in probably all two or more layer designs.