Modeling 3-center-2-electron bonds in Avogadro
First of all, I am not an Avogadro developer, just an occasional user. My view of this matter is the following:


As 3D molecular drawing/editing software, Avogradro, does not need to "understand" B-H-B bonds. If it allows you to draw them in a sensible way, it is already fulfilling its function as a drawing/editing program.
Avogadro is also an interface to a number of codes, either internal or external, that allow you to perform tasks such as geometry optimisations and conformational sampling. Now, there becomes relevant whether or not those methods can "understand" B-H-B bonding. Ab initio and other quantum mechanical methods should afford a reasonable treatment of such molecules, provided that an appropriate level of theory is used, whereas for semi-empirical and molecular mechanics methods it will depend on whether or not a given parametrisation model or a given the force field (version), respectively, have been parametrised to take such situations into account.


In summary, if you are able to draw and edit the structure in Avogadro, the real question is whether or not you are going to do something else with it within Avogadro and whether or not your method of choice is appropriate to treat your molecular systems.