This is a fascinating question, and as some of the other answers indicate, it has been taken up by an almost dizzying array of philosophers, both from the perspective of moral and political theory.
But probably the foremost political philosopher who discusses the suspension of civil liberties during a "state of war" is the Italian philosopher, Giorgio Agamben.
Specifically, he uses the term "state of exception" (also translated as "state of emergency") for what your question refers to as a "state of war", and argues that such a situation is often used as a justification for suspending the normal functions of the government in protecting the rights of citizens.
Agamben draws heavily here upon the previous work of German thinker Carl Schmitt, both in his definition of "sovereignty" and in the meaning of the term "state of exception". Schmitt argues that sovereignty is really the power of a government to declare a state of emergency. For background reading on his theories, look into what is probably his most famous work, The Concept of the Political.
Using Schmitt's terminology and conceptual background, Agamben comes out as a strong critic of modern uses of the "state of exception" as a justification for suspending civil liberties and other important rights. His aptly-titled book, State of Exception, argues that times of crisis have historically and currently allowed governments to increase their power over citizens well over what the law and previous legal precedent actually allows. Acting under the state of exception, in which a government is responding to a supposedly mortal threat, the state can do things that would never be justifiable in normal times, given the working principles and rule of law of that particular state. The state of exception employs justifications that work only in extremes in order to allow the state's own principles to be violated in order for it to save itself.
And Agamben doesn't merely write theoretically: He writes specifically about the military order issued by United States President George W. Bush in November of 2001 ("Detention, Treatment, and Trial of Certain Non-Citizens in the War Against Terrorism"), where he specifically defines the category of citizens which are subject to this order, and provides that those labeled as "enemy combatants", despite their status as U.S. citizens, could be detained and tried in military tribunals. It is a very specific and very close-to-home example (at least for many of us in the Western world) of how civil rights and liberties are suspended under the state of exception.
Here's a fairly simple summary/introduction to his arguments made in State of Exception :
The state of exception is not a dictatorship (whether constitutional or unconstitutional, commissarial or sovereign) but a space devoid of law, a zone of anomie in which all legal determinations—and above all the very distinction between public and private—are deactivated. Thus, all those theories that seek to annex the state of exception immediately to the law are false; and so too are both the theory of necessity as the original source of law and the theory that sees the state of exception as the exercise of a state’s right to its own defense or as the restoration of an originary pleromatic state of the law (“full powers”). But fallacious too are those theories, like Schmitt’s, that seek to inscribe the state of exception indirectly within a juridical context by grounding it in the division between norms of law and norms of the realization of law, between constituent power and constituted power, between norm and decision. The state of necessity is not a “state of law,” but a space without law (even though it is not a state of nature, but presents itself in the anomie that results from the suspension of law). This space devoid of law seems, for some reason, to be so essential to the juridical order that it must seek in every way to assure itself a relation with it, as if in order to ground itself the juridical order necessarily had to maintain itself in relation with an anomie. On the one hand, the juridical void at issue in the state of exception seems absolutely unthinkable for the law; on the other, this unthinkable thing nevertheless has a decisive strategic relevance for the juridical order and must not be allowed to slip away at any cost. The crucial problem connected to the suspension of the law is that of the acts committed during the institium, the nature of which seems to escape all legal definition. Because they are neither transgressive, executive, nor legislative, they seem to be situated in an absolute non-place with respect to the law. The idea of a force-of-law is a response to this undefinability and this non-place. It is as if the suspension of law freed a force or a mystical element, a sort of legal mana (the expression is used by Wagenvoort to describe the Roman auctoritas [Wagenvoort 1947, 106]), that both the ruling power and its adversaries, the constituted power as well as the constituent power, seek to appropriate. Force of law that is separate from the law, floating imperium, being-in-force [vigenza] without application, and, more generally, the idea of a sort of “degree zero” of the law—all these are fictions through which law attempts to encompass its own absence and to appropriate the state of exception, or at least to assure itself a relation with it.
– Agamben, Giorgio. State of Exception (2005). p. 61
If you're interested in this sort of theory, State of Exception is a thoroughly worthwhile read. If you have no prior exposure to Agamben's concept of homo sacer or the theory of "bare life", you may feel a bit lost, as he starts criticizing the state of exception in terms of its ability to deprive people of citizenship and divide the body into two poles—bios and zoe. For conceptual background on this, you'd need to read through his earlier book, Homo Sacer: Sovereign Power and Bare Life.