First, I should say that I don't know the answer to your question, but the 1654-1664 period is very early in the history of Quakerism, so traditions and norms were probably still forming regarding issues such as the formalisms of marriage certificates. However, women played remarkably prominent roles in Quaker leadership and governance from the very beginning -- in fact, if I'm not mistaken I believe Margaret Fell actually originated many of the Quaker patterns of governance, and women were widely considered to be the co-equals of men, at least in spiritual and religious matters. In fact, along with George Fox (who eventually became her husband after she was widowed), Fell is sometimes considered to be a co-founder of Quakerism. Thus, what surprises me is not that women were co-signatories with men but that you say it appears that married women were not. The marriage certificates I have seen from not much later than that (1670s) included women in approximately co-equal numbers with men among the witnesses, and clearly included wives, widows, unmarried women and even youth of both sexes (although women at that stage often signed in a separate section rather than alongside their husbands and families as seems to have become the norm later on). In any case, I would be profoundly surprised if there were any formalized norm excluding the witnessing of marriages by women of any status.
Assuming your observation of the Lincolnshire certificates is accurate, I wonder if the lack of signatures of married women from that early period may simply reflect lack of access to education and therefore literacy among women of that generation? Quakers of later generations were quite serious about education and making it available to girls as well as boys, but these would have been first generation Quakers. At that early stage (1650's and early 60's) they may have been just beginning to organize their own education system, and thus I would guess that literacy (or lack thereof) for mature women of that era may well have depended on the norms of wider society during their pre-Quaker upbringing. However, this hypothesis does not seem consistent with your observation that widows often signed in their own names, so I guess the bottom line is that I really don't know. Have you compiled enough certificates to really be quite sure that married women did not sign? Are you sure that it is not merely a fluke of a couple marriages or an idiosyncrasy of one or two meetings?
