Alright, your concern is "04R, 09, and 22L".

Good news first, according to 2008 figures in a [Massport][1] (Massachusetts Port Authority) report concerning RSAs, runway 09 is not used by jets for landing. I checked the 2019 numbers (2020 was Covid-hit and thus low traffic) and again 09 was not used by jets for landing.

04R and 22L are one physical runway, and each end features a long displaced threshold, which satisfies the undershoot requirements (arriving too low compared to the optimum glide path), and the same physical runway is fairly long for most landings with declared landing distances of ~8,800 ft; total length is 10,006 ft ([skyvector.com][2]).

Given the current status if unchanged further (as @mins comments there are talks or plans of a new EMAS), in bad weather conditions and low braking action and big planes needing long runways, the safest configuration (runway(s) in use) will be chosen, and **not all need have EMAS:**

Why? Because – according to the same report and FAA requirements – it is decided on on a case-by-case basis and "to the extent feasible":<sup>\[1]</sup>

>Today, modifications to standards **no longer apply to RSAs.** The airport owner and the FAA must continually analyze a non-standard RSA with respect to operational, environmental, and technological changes and revise the determination as appropriate.
>
>— FAA [AC 150/5300-13A][3]; 9/28/2012 [emphasis added]

Examples:

* The length of 04R/22L is most likely a big plus in terms of operational assessments.
* The Boeing 747's RSA requirements are why an older EMAS was replaced by a [bigger EMAS on a new pier][4] for departure end of runway ([DER][5]) 15R.
* There could very well be restrictions on using 09 for departures (29.9% of all 2019 departures) when too wet/icy in fear of a miscalculated rejected takeoff distance.

Regardless of the specifics of the assessments, the bottom line is EMAS is **not** immediately required on all those runway per the FAA.

***

References and further reading:

1. Massport report: EOEA No. 14442 ([PDF][6]; massport.com)
2. Excel file for 2019 [BOS runway usage][7] ([.xlsx][8]; massport.com)


  [1]: https://en.wikipedia.org/wiki/Massachusetts_Port_Authority
  [2]: https://skyvector.com/airport/BOS/General-Edward-Lawrence-Logan-International-Airport
  [3]: https://www.faa.gov/airports/resources/advisory_circulars/index.cfm/go/document.current/documentNumber/150_5300-13
  [4]: https://aviation.stackexchange.com/a/89138/14897
  [5]: https://aviation.stackexchange.com/a/78189/14897
  [6]: https://www.massport.com/media/2263/loganrsa_draftea_eir.pdf
  [7]: https://www.massport.com/logan-airport/about-logan/noise-abatement/runway-use/
  [8]: https://www.massport.com/media/4041/2019-annual-rw-for-supplemental-posting.xlsx