I would suspect there are a number of factors which would prevent commercialization of lypholized bio-fertilizer. The primary factor would be cost. Lypholization (freeze drying in my understanding of the term) is generally considered to be fairly expensive. As the process first requires freeze drying equipment. This would include a vessel capable of high vacuum, a method of pulling a sufficient level of vacuum at the desired volume, and a method of cooling sufficient to the level of vacuum to lead to the desired sublimation of water. As the cooling and vacuum are related functions the exact level of vacuum vs cooling varies. This process then requires repeated cycling through warming and cooling cycles to remove the water which is present. In large batches this would take a very long period of time as well as large amounts of energy. In order for fertilizer of any sort to be economically viable it must have a cost which justifies its use. The economic viability of lypholized fertilizer is probably very low. In addition depending on what you mean by "bio-fertilizer" it may or may not alter the composition. Some biological fertilizers contain live micro organisms, while some might survive lypholization others might not.
Liquid suspensions, solutions, emulsions etc. are generally employed for ease of use, The fertilizer is simply sprayed, pumped or otherwise applied through liquid handling equipment. Measuring liquids is generally easy, accurate and efficient. Lypholized powders would require either rehydration or application as a powder. Application of powders can be extremely variable and can be negatively influenced by equiptment, humidity and other forms of moisture, operator error, wind, etc. This is why solid carriers are employed for dry products. The carrying agent allows for a more uniform application.
Liquid fertilizers are most likely employed as they are cost effective and efficient to utilize. As plants utilise nutrients in solution, the use of water based fertilizers applies the nutrients in a vehicle that may be utilized by plants.
Lypholization is extremely efficient for the storage and transport of certain materials but at this point it is probably far too expensive to be cost effective when applied to fertilizer
In addition to the details written by David G Beleski, you may find useful information in the following Review Article and website.
(1) E. Malusá et al (2012) Technologies for Beneficial Microorganisms Inocula Used as Biofertilizers. The Scientific World Journal. Volume 2012 (2012), Article ID 491206, 12 pages
(2) Webpage Indo-Swiss Collaboration in Biotechnology Biofertilizer
In addition to above mentioned, its difficult to farmers to use biofertilizer in Lypholized form especially in developing countries. In Sudan we successfully commercialize biofertilizers in a carrier based form