There are two meta-principles here.
If in doubt possibly ambiguous notation should be explained. That can be done concisely and just once. Explaining your notation is good scientific and mathematical manners and essential if you want to be easily understood (we won't discuss the opposite case). There are common-sense limits to this. Depending on context and likely readership, you might not need to explain that $\pi$ is the number 3.14159... or even that $\Gamma()$ means the gamma function. Someone who wanted to explain $+$ and $-$ as addition or subtraction would be regarded with puzzlement by reviewers and editors unless they were addressing elementary audiences or trying to be ultra-rigorous about something fundamental.
Individual journals, publishers and/or societies may have a preferred house style, which always takes precedence even when it is ill-advised. If you dislike it, publish elsewhere, or become the Editor and change it.
But what you were told about logarithms (by whom? or where? what reason to respect their views?) seems to me poor advice.
I have been using $\ln$ as one notation for natural logarithms for 50 years and never come across any prejudice that it is not acceptable in written scientific English. According to one common story, $\ln$ notation was invented by an American mathematician! See e.g. this thread on Mathematics SE.
What I have found is a pure mathematical prejudice that logarithms should be written $\log$. That is expressed in Paul Halmos' autobiography, for example. In such circles, $\log$ is regarded as the only notation needed and $\ln$ or $\log_{10}$ as the resort of oily- or muddy-handed scientists and engineers.
Conversely, in a statistical context I would recommend explicit use of $\log_{10}$ if that is what you are using. Loosely, the more statistics you use, the more likely it is that logarithms mean to you natural logarithms, so that $\log$ defaults to meaning natural logarithms. This is largely because any argument based directly or indirectly on differential and integral calculus is immensely cleaner and simpler using natural logarithms $\ln$ or $\log$ as inverse to exponentiation.
The main benefit of $\ln$ is that, assuming only a good high school mathematical background, it is immediately clear what it means.