...that .shp is mainly used with GIS software which tend to not contain any indoor layouts.
Although it may only be used in certain industries, some GIS solutions and data models are specifically designed to handle 'indoor' features. For example, GE Smallworld's 'internal worlds' concept that allows modeling of the internal structures of electrical sub-stations, gas/water/oil valve stations, etc.
Second, Shapefiles are just a specific format for storing GIS data. Saying they can't store indoor data would be similar to saying you can't store a talk radio podcast in MP3 format because it's for music.
The question of 'will it work?' really comes down to how you are trying to use the data and what format your data is in.
If your goal is to simply add internal layouts to the existing buildings that you have, you could draw them in as needed, using GIS or any other tool that supports shapefiles (ie. CAD).
The only issue that comes to mind is projection/coordinate systems. If your buildings are in a geographic projection (lat/longs) then precision and measuring distances could become an issue. But that can also be addressed through using a different projection, which would be worthy of a different question (there are many here already, in fact).
You could even have each building layout in it's own shapefile, with it's own coordinate system, if you really wanted. Again, it's really down to what you are trying to accomplish.