1. Yes, it is possible to cast doubt on any relationship without DNA confirmation. Until we have a decent-sized control group of Plantagenet Y-chromosomal DNA, we shall have to content ourselves with more conventional documentary and circumstantial evidence. Has anyone written about and provided evidence for the idea that both King Henry and Count Hamelin might have been fathered by someone other than Geoffrey Plantagenet?
Given what I have seen so far, my view remains:
a) Hamelin was acknowledged by the Plantagenets and their contemporaries as a son of Geoffrey d'Anjou and brother of King Henry, and was treated accordingly (approved to marry an unusually rich heiress with English, French and Scottish royal blood; given, in addition to the vast de Warennia holdings, lands belonging to Geoffrey Plantagenet in Touraine along with the junior Angevin title Vicomte de Touraine; honored as a leading participant in the coronations of his ostensible nephews King Richard and King John; appointed a Privy Councillor; given charge of the strategically important Chateau de Lewes and Chateau de Conisborough, made a commissioner to collect King Richard's ransom, and allowed to publically bear the Escarbuncle d'Anjou on his shield and on the official seal he used on legal documents, inter alia, which seems to me to be about what one would expect for an acknowledged illegitimate half-brother of one the the most powerful Kings in Europe).
b) Matilda, from what accounts I've read, seems to have been rather conservative, arrogant, with a knack for making herself unpopular, and highly jealous of her rights and willing to sacrifice and take risks to secure them. Although her pride may have been stung by having been matched with a Count after having been Empress of the Holy Roman Empire, I have seen no evidence that she was ever promiscuous or willing to take such risks as might compromise her and her successors claims to England (which claims depended, to no small degree, on her ability to press them by military force). On the contrary, she strikes me as the type that would do her dutyby rationally aligning herself with a militarily gifted family whose French holdings were soon to surpass those of the French King's, and who could help her make good on her claim to England.
It seems to me that Matilda's claim to England was a perfect match for Angevin ambitions and talents, and that Matilda's need for powerful military and political backing was perfectly served, in turn, by her making common cause with the Angevins. It would seem to me that it would not be in Matilda's interest to compromise the political bargain she had struck with a family as powerful as the Angevins. Nor does it seem realistic to me that the Angevins would tolerate, much less take risks fighting for anyone other than King Fulk's, and Duke Geoffrey's heir to be placed on the English throne given how realizable that goal had become with Geoffrey's marriage to Matilda.
2. Good sources for relevant documents are the British Museum (they have the Registry of the Priory of Lewes; Calendarium Genealogicum; and the Calendars of Patent Rolls f. ex.), and the Archives of the Tower of London. Dugdale's "Monasticon Anglicanorum", however, is probably a more convenient source for a number of Warren charters. I would recommend Count Edouard de Warren's "Notice Historique et Genealogique sur la Famille de Warren"; Count Lucien de Warren's "Les Comtes de Warren"; and Count Raoul de Warren's"Histoire de la Maison de Warren" for particular citations of charters and cartularies, but they are harder to find than Watson's "Memoirs of the Ancient Earls..."
You may certainly use my citation of Count Raoul de Warren's "La Maison de Warren 1138-1964" (private printing, Paris 1964) which is a summary of his much more detailed but unpublished "Histoire". On pp. 57-58 de Warren writes: "Il [Hamelin] assista aux couronnements des rois Richard Coeur-de-Leon et Jean-sans-Terre, ses neveux, et fut membre du Conseil Prive du Royaume. Il est designe dans les actes comme "Hamelinus, Comes de Warren, Regis Henrici Frater." This seems to indicate Hamelin was designated the King's brother in acta of the Privy Council; whether Henry's, Richard's, or John's we are left to wonder.
3. For what its worth (I know they could all be wrong, but I would say the burden of proof is perhaps on the skeptic at this point), here are a few of the authorities that accept the accuracy of the historical record regarding Hamelin de Warren's paternal origins among the Angevin Counts:
a) Herald's Office, College of Arms, London (contains offically attested pedigrees of the this line).
b) Ulster's Office of Arms, College of Arms, Dublin (contains officially attested pedigrees of this line).
c) Association d'Entraide de la Noblesse Francaise (ANF) anorganization in Paris comprised of the authentic nobility of France that archives the pedigrees of the nobility. They have an officially attested pedigree of the this line.
c) The Oxford Dictionary of National Biography
d) Dugdale's "Baronage of England"
e) Burke's "Dormant and Extinct Peerages" 1866
f) Marquis de Ruvigny's "The Titled Nobility of Europe" 1914
g) Anselme's "Batards d'Anjou, Comtes de Varennes et Surrey" from his "Histoire Genealogique des Souverains de France"