Biometric systems commonly utilize multi-biometric approaches where a person is verified or identified based on multiple biometric traits. However, requiring systems that are deployed usually require verification or identification from a large number of enrolled candidates. These are possible only if there are efficient methods that retrieve relevant candidates in a multi-biometric system. To solve this problem, we analyze the use of hashing techniques that are available for obtaining retrieval. We specifically based on our analysis recommend the use of supervised hashing techniques over deep learned features as a possible common technique to solve this problem. Our investigation includes a comparison of some of the supervised and unsupervised methods viz. Principal Component Analysis (PCA), Locality Sensitive Hashing (LSH), Locality-sensitive binary codes from shift-invariant kernels (SKLSH), Iterative quantization: A procrustean approach to learning binary codes (ITQ), Binary Reconstructive Embedding (BRE) and Minimum loss hashing (MLH) that represent the prevalent classes of such systems and we present our analysis for the following biometric data: Face, Iris, and Fingerprint for a number of standard datasets. The main technical contributions through this work are as follows: (a) Proposing Siamese network based deep learned feature extraction method (b) Analysis of common feature extraction techniques for multiple biometrics as to a reduced feature space representation (c) Advocating the use of supervised hashing for obtaining a compact feature representation across different biometrics traits. (d) Analysis of the performance of deep representations against shallow representations in a practical reduced feature representation framework. Through experimentation with multiple biometrics traits, feature representations, and hashing techniques, we can conclude that current deep learned features when retrieved using supervised hashing can be a standard pipeline adopted for most unimodal and multimodal biometric identification tasks.