Was there ever any mixing up of 阙 and 缺 for the meaning of 'lack' or 'short of'? 阙 in 现代汉语大词典 says

quē
[....]
4 缺乏；稀少。

with the excerpt:

鲁迅《狂人日记》
分隔多年, 消息渐阙。

Which seems strikingly similar to the pronunciation and meaning of:
缺:

quē
[....]
3 短少。
鲁迅《牺牲谟》
现在什么‘欧化’‘美化’的邪说横行, 人们的眼睛只看见物质, 所缺的就是你老兄似的模范人物。

The two characters pronunciation in Cantonese seem to be the same (kyut3) and Middle Chinese reconstructed pronunciations also seem to be the same (khwet).
Is it possible that there was ever any sort of 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.