Was there ever any mixing up of 阙 and 缺 for the meaning of 'lack' or 'short of'?
They were definitely context-dependent variant representations of a single word and interchangeable to a large degree. According to various dictionaries that Pleco references in its entry to「闕」:


Pleco Chinese-English (PLC): Variant of 缺
CC-CEDICT (CC): Used in place of 缺 (old)
Cross-Straits (LAC): 脫漏。通「缺」。
MOEDict (MOE): 脫漏的。闕字有二音，音ㄑㄩㄝ時義同「缺」。但使用習慣上仍見分別，如「拾遺補闕」、「疑闕」、「闕文」專詞多作「闕」，少用「缺」。


The last definition describes the modern usage differences between the two.

Note that to lack is unlikely to be the original meaning of either「闕」or「缺」:


闕, 門觀也。从門，欮聲。〔去月切〕(Basically,「闕」is a watchtower on a city wall; this is the Shuowen definition and AFAIK there's no evidence contradicting this.)
「缺」：從「缶」，「夬」聲。本義是器物破損。〔傾雪切〕


To lack could be interpreted as an extension of the original meaning of「缺」, and sometimes authors used「闕」for this meaning instead as a phonetic loan. Later on, the usage of「闕」and「缺」somewhat became differentiated.