Can a person be arrested/detained if a prohibited item is found in the carry-on luggage while transiting?

1. Either the knife was not noticed, or the blade was considered short enough to pass under Russian rules. This is irrelevant though: just because I can legally bring an apple through security in Singapore doesn't mean Customs is obliged to let it through in Australia.
2. The consequences of having prohibited items depends on local law and the discretion of the screeners. Being in transit is irrelevant.
3. Absolutely: even in transit, you are subject to Kazakh law. For example, Singapore regularly executes drug smugglers caught in transit.
4. Possibly, although if so, I would have expected them to hint at this. Bribery is also difficult if there are multiple officers and security cameras etc involved, which would be the case at an airport.
5. Highly unlikely. The confiscation was carried out by airport security, you were not arrested or charged with a crime.

While I certainly understand your concerns about signing something you don't understand, in this particular case it's nothing to worry about.

Obviously, full name of the passenger, flight number, details and signature of the person who made [sic] the protocol are obvious. The parts in Russian say:

Flight number 907 on the route Deli
Found and seized knife 1 item (KNIFE)

Now, to answer your questions...

Why wasn’t the knife taken out at Russian airport ?

Most likely, security just missed it. You yourself said that it was a small knife - the security person in Pulkovo could have been tired or for any other reason missed it - that's all to it.

Were we made to sign only because we were in transit and had completed one part of journey with the knife in carry on baggage?

This had nothing to do with transit. You were required to sign a piece of paper confirming that an item was seized. If you didn't sign it, you could then claim that this item was stolen by security personnel or what not. This way, there is a proof - both for you and the airport personnel that a prohibited item was seized from you.

Can carrying a prohibited item result in detention or arrest?

It certainly could. Note that while in any airport, you are within the Jurisdiction of the country where the airport is located. Now, if restricted means illegal in the country, then absolutely, you can (and most likely will be) arrested, charged with possession of illegal items - and the police/courts would take it from there. If on the other hand it means prohibited in hand luggage but otherwise legal, then very unlikely.

Was the policeman interested in taking bribe by intimidating us?

Extremely unlikely. The more likely scenario was that he was just annoyed that you were wasting his time, as he was simply following a standard protocol, dealing with something probably boring (in his police view, maybe) and wanted to be done with this.

If they wanted a bribe, they would typically say you have to pay a fine. Then you would discover that actually paying the fine requires you to do something that is incompatible with your journey (like obtaining a form from the bank, which would make you miss your next flight). Of course, they would offer you an already filled form right in the airport, but you'd have to pay in cash and get no receipt.

Your incident doesn't look like an attempt to get a bribe, the airport officials were simply annoyed that they had to spend time on these forms, which would explain the rudeness. They also refused to call you an interpreter since they decided you didn't need one for a simple item seizure protocol.

Unfortunately, you weren't told sections 38 and 40 of which law were applied to you, so it's hard to say what repercussions the incident may have on your future trips. Considering your knife was simply seized and no fine or court presence was due, I would hazard a guess that there will be none.