Is there any language which doesn't have "hello", "thank you" or "please"?

This is really a question at the intersection of language and culture. It has nothing to do with proto-language or much to do with language as such. When you ask for words for 'hello' or 'thank you', you really encounter a whole lot of ways for people to manage interactions that gave rise to how those words are used in present-day English.

Every culture has to manage contexts where people acknowledge each others' actions. This could be simply coming into each other's presence or exchanging gifts, asking for assistance, etc. The situations will vary and the cultural means will vary.

In some cultures, it is impolite to acknowledge certain acts (e.g. by some expression of gratitude) but it maybe equally impolite not to reciprocate that action. Conversely, in other cultures profuse verbal thanks are the norm even in acknowledgements of mundane interpersonal acts.

One example of this is the US where many Europeans end up being slightly rude simply by not saying thank you as often. This is not a clear difference between having or not having an expression or even a shared context of using it - it is simply a question of degree which can cumulatively impact interpersonal relationships.

The same goes for things like greetings. It is not just a matter of having a word for 'hello'. It is also a question of when you use it, to whom and how. For instance, in many European cultures it is expected that one says 'hello' when entering public spaces (waiting rooms, smaller shops) with a smaller number of other people to utter a formal greeting (not just a universal 'hello') and to say some form of 'good bye' on leaving. No other interaction is expected. For instance, in the Czech culture it is common (less so now under Western influences) to join people at a table in a full restaurant. It is obligatory to say hello and good bye (both formal) but no other words maybe exchanged. In American English, for instance, a greeting is almost always used as a prelude to some social interaction.

So when you say is there a word for 'hello' in both languages it may seem yes on the surface but when you look at the variation in usage and forms (Czech has more contextual ways) you must really say no. These differences become much more pronounced when it comes to language whose cultures have had less contact. And of course, you also need to take into account gestures and facial expressions that need to accompany these cultural acts of interaction.

As far as etymologies go, if you look across languages you will see that there is an enormous amount of borrowing and analogies in forms for greetings. They usually derive from some sort of wish of good fortune or health (bonjour, guttentag, zdravstvujte) or inquiry after well-being (ni hao) on the more formal end. On the more informal end you see some expression of solidarity or subservience (servus, ciao) or getting attention (hello, ahoy) but also often borrowing (ciao or hi is becoming popular across some cultures). Religious origins can also be seen in some greetings (good bye, Grüß Gott).

The forms for thanking are much more complex because expressions of gratitude are much more complex and varied across languages than simple greetings (which are complex enough).