The same can obviously not really be said of क्ष, which does not seem based on क or ष at all and, if it is, then all remnants of them have become masked over time. Even in the case of really complicated ligatures, like the famous ddhrya ligature, there is a fairly clear rhyme and reason to them and it's usually possible to deduce what they represent with practice. त्स, for example, is obviously त् + स, म्प is obviously म् + प. I don't know anything about this, I really don't, but it could be that most ligatures in Devanagari are more or less obviously derived from their component characters according to regular rules. When a loan-word is adopted into a language using the same script, the way of writing is likely to be followed. I don't think Sanskrit sounds were ever written without these and other ligatures taking refuge in the viraama since the time Sanskrit writers adopted Devanagari script so that may be the reason for their retainment. These three, that is tra, jn'a and kSHa, have been retained in the computer systems because they are needed for New Indic languages in the loanwords from Sanskrit. I remember having learnt another form for 'kSHa', Na, jha. These ligatures, as dozens of others, have been devised and evolved with time perhaps due to the factors of the means the scribes used to write them down, their acceptability and being distinguished from other shapes. The same goes for 'tra' त्र and the other form which can't be reproduced on this system but which includes the full त with an inside 'r' symbol. As can be seen, there are two variants of the ligature nn(a) as presented above. The word जानना which is Hindi for 'to know' would have to be written in Sanskrit as जान्ना or जान्ना. There are many more ligatures like this which are used for Sanskrit and the other languages but Sanskrit due to phonetical accurateness requires them in order to represent the correct pronunciation of a word. For I am not able to answer this question right away, I would like to note that those symbols are not strictly speaking 'letters' but 'ligatures' of letters (or symbols, which contain the inherent final schwa in the case of Marathi, Sanskrit and sometimes Hindi, I don't know anything about Nepalese).

Alphabet letters in hindi